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1.132-3.368.397-.406.89-.717 1.474-.952 1.399-1.136 3.392-2.093 6.122-2.093 2.731 0 4.767.957 6.166 2.093.584.235 1.077.546 1.474.952.85.869 1.132 2.037 1.132 3.368 0 .368-.014.733-.052 1.086.23.462.477 1.088.644 1.517 1.258.364 2.233 1.721 2.605 2.656a.832.832 0 0 1 .053.22v2.869a.641.641 0 0 1-.078.256ZM12.172 11h-.344a4.323 4.323 0 0 1-.355.508C10.703 12.455 9.555 13 7.965 13c-1.725 0-2.989-.359-3.782-1.259a2.005 2.005 0 0 1-.085-.104L4 11.741v6.585c1.435.779 4.514 2.179 8 2.179 3.486 0 6.565-1.4 8-2.179v-6.585l-.098-.104s-.033.045-.085.104c-.793.9-2.057 1.259-3.782 1.259-1.59 0-2.738-.545-3.508-1.492a4.323 4.323 0 0 1-.355-.508h-.016.016Zm.641-2.935c.136 1.057.403 1.913.878 2.497.442.544 1.134.938 2.344.938 1.573 0 2.292-.337 2.657-.751.384-.435.558-1.15.558-2.361 0-1.14-.243-1.847-.705-2.319-.477-.488-1.319-.862-2.824-1.025-1.487-.161-2.192.138-2.533.529-.269.307-.437.808-.438 1.578v.021c0 .265.021.562.063.893Zm-1.626 0c.042-.331.063-.628.063-.894v-.02c-.001-.77-.169-1.271-.438-1.578-.341-.391-1.046-.69-2.533-.529-1.505.163-2.347.537-2.824 1.025-.462.472-.705 1.179-.705 2.319 0 1.211.175 1.926.558 2.361.365.414 1.084.751 2.657.751 1.21 0 1.902-.394 2.344-.938.475-.584.742-1.44.878-2.497Z"></path><path d="M14.5 14.25a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Zm-5 0a1 1 0 0 1 1 1v2a1 1 0 0 1-2 0v-2a1 1 0 0 1 1-1Z"></path> </svg> <div> <div class="color-fg-default h4">GitHub Copilot</div> Write better code with AI </div> </a></li> <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description pb-lg-3" data-analytics-event="{"location":"navbar","action":"security","context":"product","tag":"link","label":"security_link_product_navbar"}" href="https://github.com/features/security"> <svg aria-hidden="true" height="24" viewBox="0 0 24 24" version="1.1" width="24" data-view-component="true" class="octicon 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href="https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax" data-view-component="true" class="Link color-fg-accent text-normal ml-2"> Search syntax tips </a> <div class="d-flex flex-1"></div> </div> </div> </div> </div> </modal-dialog></div> </div> <div data-action="click:qbsearch-input#retract" class="dark-backdrop position-fixed" hidden data-target="qbsearch-input.darkBackdrop"></div> <div class="color-fg-default"> <dialog-helper> <dialog data-target="qbsearch-input.feedbackDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="feedback-dialog" aria-modal="true" aria-labelledby="feedback-dialog-title" aria-describedby="feedback-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll"> <div data-view-component="true" class="Overlay-header"> <div class="Overlay-headerContentWrap"> <div 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method="post"><input type="hidden" data-csrf="true" name="authenticity_token" value="50YFS/bgzJjyEHQwVxtRZwnwvi6m1gPxfv4EYpneOP9/FxTWDvIn42gvOJM5N2HJfqgyZy246lFeUzzdD44Zug==" /> <p>We read every piece of feedback, and take your input very seriously.</p> <textarea name="feedback" class="form-control width-full mb-2" style="height: 120px" id="feedback"></textarea> <input name="include_email" id="include_email" aria-label="Include my email address so I can be contacted" class="form-control mr-2" type="checkbox"> <label for="include_email" style="font-weight: normal">Include my email address so I can be contacted</label> </form></div> </scrollable-region> <div data-view-component="true" class="Overlay-footer Overlay-footer--alignEnd"> <button data-close-dialog-id="feedback-dialog" type="button" data-view-component="true" class="btn"> Cancel </button> <button form="code-search-feedback-form" data-action="click:qbsearch-input#submitFeedback" type="submit" data-view-component="true" class="btn-primary btn"> Submit feedback </button> </div> </dialog></dialog-helper> <custom-scopes data-target="qbsearch-input.customScopesManager"> <dialog-helper> <dialog data-target="custom-scopes.customScopesModalDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="custom-scopes-dialog" aria-modal="true" aria-labelledby="custom-scopes-dialog-title" aria-describedby="custom-scopes-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll"> <div data-view-component="true" class="Overlay-header Overlay-header--divided"> <div class="Overlay-headerContentWrap"> <div class="Overlay-titleWrap"> <h1 class="Overlay-title " id="custom-scopes-dialog-title"> Saved searches </h1> <h2 id="custom-scopes-dialog-description" class="Overlay-description">Use saved searches to filter your results more quickly</h2> </div> <div class="Overlay-actionWrap"> 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data-target="react-partial.embeddedData">{"props":{"initialPayload":{"allShortcutsEnabled":false,"path":"/","repo":{"id":81784329,"defaultBranch":"master","name":"Porechop","ownerLogin":"rrwick","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2017-02-13T04:20:00.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/7053555?v=4","public":true,"private":false,"isOrgOwned":false},"currentUser":null,"refInfo":{"name":"master","listCacheKey":"v0:1517184620.0","canEdit":false,"refType":"branch","currentOid":"109e437280436d1ec27e5a5b7a34ffb752176390"},"tree":{"items":[{"name":"misc","path":"misc","contentType":"directory"},{"name":"porechop","path":"porechop","contentType":"directory"},{"name":"test","path":"test","contentType":"directory"},{"name":".gitignore","path":".gitignore","contentType":"file"},{"name":"LICENSE","path":"LICENSE","contentType":"file"},{"name":"MANIFEST.in","path":"MANIFEST.in","contentType":"file"},{"name":"Makefile","path":"Makefile","contentType":"file"},{"name":"README.md","path":"README.md","contentType":"file"},{"name":"ez_setup.py","path":"ez_setup.py","contentType":"file"},{"name":"porechop-runner.py","path":"porechop-runner.py","contentType":"file"},{"name":"setup.py","path":"setup.py","contentType":"file"}],"templateDirectorySuggestionUrl":null,"readme":null,"totalCount":11,"showBranchInfobar":false},"fileTree":null,"fileTreeProcessingTime":null,"foldersToFetch":[],"treeExpanded":false,"symbolsExpanded":false,"isOverview":true,"overview":{"banners":{"shouldRecommendReadme":false,"isPersonalRepo":false,"showUseActionBanner":false,"actionSlug":null,"actionId":null,"showProtectBranchBanner":false,"publishBannersInfo":{"dismissActionNoticePath":"/settings/dismiss-notice/publish_action_from_repo","releasePath":"/rrwick/Porechop/releases/new?marketplace=true","showPublishActionBanner":false},"interactionLimitBanner":null,"showInvitationBanner":false,"inviterName":null,"actionsMigrationBannerInfo":{"releaseTags":[],"showImmutableActionsMigrationBanner":false,"initialMigrationStatus":null}},"codeButton":{"contactPath":"/contact","isEnterprise":false,"local":{"protocolInfo":{"httpAvailable":true,"sshAvailable":null,"httpUrl":"https://github.com/rrwick/Porechop.git","showCloneWarning":null,"sshUrl":null,"sshCertificatesRequired":null,"sshCertificatesAvailable":null,"ghCliUrl":"gh repo clone rrwick/Porechop","defaultProtocol":"http","newSshKeyUrl":"/settings/ssh/new","setProtocolPath":"/users/set_protocol"},"platformInfo":{"cloneUrl":"https://desktop.github.com","showVisualStudioCloneButton":false,"visualStudioCloneUrl":"https://windows.github.com","showXcodeCloneButton":false,"xcodeCloneUrl":"xcode://clone?repo=https%3A%2F%2Fgithub.com%2Frrwick%2FPorechop","zipballUrl":"/rrwick/Porechop/archive/refs/heads/master.zip"}},"newCodespacePath":"/codespaces/new?hide_repo_select=true\u0026repo=81784329"},"popovers":{"rename":null,"renamedParentRepo":null},"commitCount":"115","overviewFiles":[{"displayName":"README.md","repoName":"Porechop","refName":"master","path":"README.md","preferredFileType":"readme","tabName":"README","richText":"\u003carticle class=\"markdown-body entry-content container-lg\" itemprop=\"text\"\u003e\u003cp align=\"center\" dir=\"auto\"\u003e\u003ca target=\"_blank\" rel=\"noopener noreferrer\" href=\"/rrwick/Porechop/blob/master/misc/porechop_logo_knife.png\"\u003e\u003cimg src=\"/rrwick/Porechop/raw/master/misc/porechop_logo_knife.png\" alt=\"Porechop\" width=\"600\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003ePorechop is a tool for finding and removing adapters from \u003ca href=\"https://nanoporetech.com/\" rel=\"nofollow\"\u003eOxford Nanopore\u003c/a\u003e reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003ePorechop also supports demultiplexing of Nanopore reads that were barcoded with the \u003ca href=\"https://store.nanoporetech.com/native-barcoding-kit-1d.html\" rel=\"nofollow\"\u003eNative Barcoding Kit\u003c/a\u003e, \u003ca href=\"https://store.nanoporetech.com/pcr-barcoding-kit-96.html\" rel=\"nofollow\"\u003ePCR Barcoding Kit\u003c/a\u003e or \u003ca href=\"https://store.nanoporetech.com/rapid-barcoding-sequencing-kit.html\" rel=\"nofollow\"\u003eRapid Barcoding Kit\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eOct 2018 update: Porechop is officially unsupported\u003c/h3\u003e\u003ca id=\"user-content-oct-2018-update-porechop-is-officially-unsupported\" class=\"anchor\" aria-label=\"Permalink: Oct 2018 update: Porechop is officially unsupported\" href=\"#oct-2018-update-porechop-is-officially-unsupported\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eWhile I'm happy Porechop has so many users, it has always been a bit klugey and a pain to maintain. I don't have the time to give it the attention it deserves, so I'm going to now officially declare Porechop as abandonware (though the unanswered \u003ca href=\"https://github.com/rrwick/Porechop/issues\"\u003eissues\u003c/a\u003e and \u003ca href=\"https://github.com/rrwick/Porechop/pulls\"\u003epull requests\u003c/a\u003e reveal that it already has been for some time). I've added a \u003ca href=\"#known-issues\"\u003eknown issues\u003c/a\u003e section to the README to outline what I think is wrong with Porechop and how a reimplementation should look. I may someday (no promises though 😛) try to rewrite it from a blank canvas to address its faults.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eTable of contents\u003c/h1\u003e\u003ca id=\"user-content-table-of-contents\" class=\"anchor\" aria-label=\"Permalink: Table of contents\" href=\"#table-of-contents\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#requirements\"\u003eRequirements\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#installation\"\u003eInstallation\u003c/a\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#install-from-source\"\u003eInstall from source\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#build-and-run-without-installation\"\u003eBuild and run without installation\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#quick-usage-examples\"\u003eQuick usage examples\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#how-it-works\"\u003eHow it works\u003c/a\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ca href=\"#find-matching-adapter-sets\"\u003eFind matching adapter sets\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#trim-adapters-from-read-ends\"\u003eTrim adapters from read ends\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#split-reads-with-internal-adapters\"\u003eSplit reads with internal adapters\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#discard-reads-with-internal-adapters\"\u003eDiscard reads with internal adapters\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#barcode-demultiplexing\"\u003eBarcode demultiplexing\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#barcode-demultiplexing-with-albacore\"\u003eBarcode demultiplexing with Albacore\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#output\"\u003eOutput\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#verbose-output\"\u003eVerbose output\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#known-adapters\"\u003eKnown adapters\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#full-usage\"\u003eFull usage\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#known-issues\"\u003eKnown issues\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#acknowledgements\"\u003eAcknowledgements\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"#license\"\u003eLicense\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eRequirements\u003c/h1\u003e\u003ca id=\"user-content-requirements\" class=\"anchor\" aria-label=\"Permalink: Requirements\" href=\"#requirements\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eLinux or macOS\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.python.org/\" rel=\"nofollow\"\u003ePython\u003c/a\u003e 3.4 or later\u003c/li\u003e\n\u003cli\u003eC++ compiler\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eIf you're using \u003ca href=\"https://gcc.gnu.org/\" rel=\"nofollow\"\u003eGCC\u003c/a\u003e, version 4.9.1 or later is required (check with \u003ccode\u003eg++ --version\u003c/code\u003e).\u003c/li\u003e\n\u003cli\u003eRecent versions of \u003ca href=\"http://clang.llvm.org/\" rel=\"nofollow\"\u003eClang\u003c/a\u003e and \u003ca href=\"https://software.intel.com/en-us/c-compilers\" rel=\"nofollow\"\u003eICC\u003c/a\u003e should also work (C++14 support is required).\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eI haven't tried to make Porechop run on Windows, but it should be possible. If you have any success on this front, let me know and I'll add instructions to this README!\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstallation\u003c/h1\u003e\u003ca id=\"user-content-installation\" class=\"anchor\" aria-label=\"Permalink: Installation\" href=\"#installation\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eInstall from source\u003c/h3\u003e\u003ca id=\"user-content-install-from-source\" class=\"anchor\" aria-label=\"Permalink: Install from source\" href=\"#install-from-source\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eRunning the \u003ccode\u003esetup.py\u003c/code\u003e script will compile the C++ components of Porechop and install a \u003ccode\u003eporechop\u003c/code\u003e executable:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"git clone https://github.com/rrwick/Porechop.git\ncd Porechop\npython3 setup.py install\nporechop -h\"\u003e\u003cpre\u003egit clone https://github.com/rrwick/Porechop.git\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e Porechop\npython3 setup.py install\nporechop -h\u003c/pre\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eNotes:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eIf the last command complains about permissions, you may need to run it with \u003ccode\u003esudo\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003eInstall just for your user: \u003ccode\u003epython3 setup.py install --user\u003c/code\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eIf you get a strange \"can't combine user with prefix\" error, read \u003ca href=\"http://stackoverflow.com/questions/4495120\" rel=\"nofollow\"\u003ethis\u003c/a\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003eInstall to a specific location: \u003ccode\u003epython3 setup.py install --prefix=$HOME/.local\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003eInstall with pip (local copy): \u003ccode\u003epip3 install path/to/Porechop\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003eInstall with pip (from GitHub): \u003ccode\u003epip3 install git+https://github.com/rrwick/Porechop.git\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003eIf you'd like to specify which compiler to use, set the \u003ccode\u003eCXX\u003c/code\u003e variable: \u003ccode\u003eexport CXX=g++-6; python3 setup.py install\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003ePorechop includes \u003ccode\u003eez_setup.py\u003c/code\u003e for users who don't have \u003ca href=\"https://pypi.python.org/pypi/setuptools\" rel=\"nofollow\"\u003esetuptools\u003c/a\u003e installed, though that script is \u003ca href=\"https://github.com/pypa/setuptools/issues/581\" data-hovercard-type=\"issue\" data-hovercard-url=\"/pypa/setuptools/issues/581/hovercard\"\u003edeprecated\u003c/a\u003e. So if you run into any installation problems, make sure setuptools is installed on your computer: \u003ccode\u003epip3 install setuptools\u003c/code\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eBuild and run without installation\u003c/h3\u003e\u003ca id=\"user-content-build-and-run-without-installation\" class=\"anchor\" aria-label=\"Permalink: Build and run without installation\" href=\"#build-and-run-without-installation\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eBy simply running \u003ccode\u003emake\u003c/code\u003e in Porechop's directory, you can compile the C++ components but not install an executable. The program can then be executed by directly calling the \u003ccode\u003eporechop-runner.py\u003c/code\u003e script.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell notranslate position-relative overflow-auto\" dir=\"auto\" data-snippet-clipboard-copy-content=\"git clone https://github.com/rrwick/Porechop.git\ncd Porechop\nmake\n./porechop-runner.py -h\"\u003e\u003cpre\u003egit clone https://github.com/rrwick/Porechop.git\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e Porechop\nmake\n./porechop-runner.py -h\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eQuick usage examples\u003c/h1\u003e\u003ca id=\"user-content-quick-usage-examples\" class=\"anchor\" aria-label=\"Permalink: Quick usage examples\" href=\"#quick-usage-examples\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003cstrong\u003eBasic adapter trimming:\u003c/strong\u003e\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz -o output_reads.fastq.gz\u003c/code\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003cstrong\u003eTrimmed reads to stdout, if you prefer:\u003c/strong\u003e\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz \u0026gt; output_reads.fastq\u003c/code\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003cstrong\u003eDemultiplex barcoded reads:\u003c/strong\u003e\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz -b output_dir\u003c/code\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003cstrong\u003eDemultiplex barcoded reads, straight from Albacore output directory:\u003c/strong\u003e\u003cbr\u003e\n\u003ccode\u003eporechop -i albacore_dir -b output_dir\u003c/code\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003cstrong\u003eAlso works with FASTA:\u003c/strong\u003e\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fasta -o output_reads.fasta\u003c/code\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003cstrong\u003eMore verbose output:\u003c/strong\u003e\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz -o output_reads.fastq.gz --verbosity 2\u003c/code\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003e\u003cstrong\u003eGot a big server?\u003c/strong\u003e\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz -o output_reads.fastq.gz --threads 40\u003c/code\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eHow it works\u003c/h1\u003e\u003ca id=\"user-content-how-it-works\" class=\"anchor\" aria-label=\"Permalink: How it works\" href=\"#how-it-works\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eFind matching adapter sets\u003c/h3\u003e\u003ca id=\"user-content-find-matching-adapter-sets\" class=\"anchor\" aria-label=\"Permalink: Find matching adapter sets\" href=\"#find-matching-adapter-sets\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003ePorechop first aligns a subset of reads (default 10000 reads, change with \u003ccode\u003e--check_reads\u003c/code\u003e) to all known adapter sets. Adapter sets with at least one high identity match (default 90%, change with \u003ccode\u003e--adapter_threshold\u003c/code\u003e) are deemed present in the sample.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eIdentity in this step is measured over the full length of the adapter. E.g. in order to qualify for a 90% match, an adapter could be present at 90% identity over its full length, or it could be present at 100% identity over 90% of its length, but a 90% identity match over 90% of the adapter length would not be sufficient.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThe \u003ca href=\"http://seqan.readthedocs.io/en/master/Tutorial/DataStructures/Alignment/ScoringSchemes.html\" rel=\"nofollow\"\u003ealignment scoring scheme\u003c/a\u003e used in this and subsequent alignments can be modified using the \u003ccode\u003e--scoring_scheme\u003c/code\u003e option (default: match = 3, mismatch = -6, gap open = -5, gap extend = -2).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eTrim adapters from read ends\u003c/h3\u003e\u003ca id=\"user-content-trim-adapters-from-read-ends\" class=\"anchor\" aria-label=\"Permalink: Trim adapters from read ends\" href=\"#trim-adapters-from-read-ends\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe first and last bases in each read (default 150 bases, change with \u003ccode\u003e--end_size\u003c/code\u003e) are aligned to each present adapter set. When a long enough (default 4, change with \u003ccode\u003e--min_trim_size\u003c/code\u003e) and strong enough (default 75%, change with \u003ccode\u003e--end_threshold\u003c/code\u003e) match is found, the read is trimmed. A few extra bases (default 2, change with \u003ccode\u003e--extra_end_trim\u003c/code\u003e) past the adapter match are removed as well to ensure it's all removed.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eIdentity in this step is measured over the \u003cem\u003ealigned part\u003c/em\u003e of the adapter, not its full length. E.g. if the last 5 bases of an adapter exactly match the first 5 bases of a read, that counts as a 100% identity match and those bases will be trimmed off. This allows Porechop to effectively trim partially present barcodes.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThe default \u003ccode\u003e--end_threshold\u003c/code\u003e is low (75%) because false positives (trimming off some sequence that wasn't really an adapter) shouldn't be too much of a problem with long reads, as only a tiny fraction of the read is lost.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eSplit reads with internal adapters\u003c/h3\u003e\u003ca id=\"user-content-split-reads-with-internal-adapters\" class=\"anchor\" aria-label=\"Permalink: Split reads with internal adapters\" href=\"#split-reads-with-internal-adapters\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe entirety of each read is aligned to the present adapter sets to spot cases where an adapter is in the middle of the read, indicating a chimera. When a strong enough match is found (default 85%, change with \u003ccode\u003e--middle_threshold\u003c/code\u003e), the read is split. If the resulting parts are too short (default less than 1000 bp, change with \u003ccode\u003e--min_split_read_size\u003c/code\u003e), they are discarded.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThe default \u003ccode\u003e--middle_threshold\u003c/code\u003e (85%) is higher than the default \u003ccode\u003e--end_threshold\u003c/code\u003e (75%) because false positives in this step (splitting a read that is not chimeric) could be more problematic than false positives in the end trimming step. If false negatives (failing to split a chimera) are worse for you than false positives (splitting a non-chimera), you should reduce this threshold (e.g. \u003ccode\u003e--middle_threshold 75\u003c/code\u003e).\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eExtra bases are also removed next to the hit, and how many depends on the side of the adapter. If we find an adapter that's expected at the start of a read, it's likely that what follows is good sequence but what precedes it may not be. Therefore, a few bases are trimmed after the adapter (default 10, change with \u003ccode\u003e--extra_middle_trim_good_side\u003c/code\u003e) and more bases are trimmed before the adapter (default 100, change with \u003ccode\u003e--extra_middle_trim_bad_side\u003c/code\u003e). If the found adapter is one we'd expect at the end of the read, then the \"good side\" is before the adapter and the \"bad side\" is after the adapter.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eHere is a real example of the \"good\" and \"bad\" sides of an adapter. The adapter is in the middle of this snippet (SQK-NSK007_Y_Top at about 90% identity). The bases to the left are the \"bad\" side and their repetitive nature is clear. The bases to the right are the \"good\" side and represent real biological sequence.\u003c/p\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"TGTTGTTGTTGTTATTGTTGTTATTGTTGTTGTATTGTTGTTATTGTTGTTGTTGTACATTGTTATTGTTGTATTGTTGTTATTGTTGTTGTATTATCGGTGTACTTCGTTCAGTTACGTATTACTATCGCTATTGTTTGCAGTGAGAGGTGGCGGTGAGCGTTTTCAAATGGCCCTGTACAATCATGGGATAACAACATAAGGAACGGACCATGAAGTCACTTCT\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eTGTTGTTGTTGTTATTGTTGTTATTGTTGTTGTATTGTTGTTATTGTTGTTGTTGTACATTGTTATTGTTGTATTGTTGTTATTGTTGTTGTATTATCGGTGTACTTCGTTCAGTTACGTATTACTATCGCTATTGTTTGCAGTGAGAGGTGGCGGTGAGCGTTTTCAAATGGCCCTGTACAATCATGGGATAACAACATAAGGAACGGACCATGAAGTCACTTCT\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eDiscard reads with internal adapters\u003c/h3\u003e\u003ca id=\"user-content-discard-reads-with-internal-adapters\" class=\"anchor\" aria-label=\"Permalink: Discard reads with internal adapters\" href=\"#discard-reads-with-internal-adapters\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf you run Porechop with \u003ccode\u003e--discard_middle\u003c/code\u003e, the reads with internal adapters will be thrown out instead of split.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eIf you plan on using your reads with \u003ca href=\"https://github.com/jts/nanopolish\"\u003eNanopolish\u003c/a\u003e, then the \u003ccode\u003e--discard_middle\u003c/code\u003e option is required. This is because Nanopolish first runs \u003ca href=\"https://github.com/jts/nanopolish#data-preprocessing\"\u003e\u003ccode\u003enanopolish index\u003c/code\u003e\u003c/a\u003e to find a one-to-one association between FASTQ reads and fast5 files. If you ran Porechop \u003cem\u003ewithout\u003c/em\u003e \u003ccode\u003e--discard_middle\u003c/code\u003e, then you could end up with multiple separate FASTQ reads which are from a single fast5, and this is incompatible with Nanopolish.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThis option is also recommended if you are trimming reads from a demultiplexed barcoded sequencing run. This is because chimeric reads may contain two sequences from two separate barcodes, so throwing them out is the safer option to reduce cross-barcode contamination.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eBarcode demultiplexing\u003c/h3\u003e\u003ca id=\"user-content-barcode-demultiplexing\" class=\"anchor\" aria-label=\"Permalink: Barcode demultiplexing\" href=\"#barcode-demultiplexing\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003ePorechop can also demultiplex the reads into bins based on which barcode was found. This is done by using the \u003ccode\u003e-b\u003c/code\u003e option, which specifies an output directory for the trimmed reads (each barcode in a separate file), instead of \u003ccode\u003e-o\u003c/code\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003ePorechop looks for barcodes at the start and end of each read. All barcode matches are found, and if the best match is strong enough (default 75%, change with \u003ccode\u003e--barcode_threshold\u003c/code\u003e) and sufficiently better than the second-best barcode match (default 5% better, change with \u003ccode\u003e--barcode_diff\u003c/code\u003e), then the read is assigned to that barcode bin. E.g. with default settings, if BC01 was found at 79% identity and BC02 was found at 76% identity, the read will not be assigned to a barcode bin because the results were too close. But if you used \u003ccode\u003e--barcode_diff 1\u003c/code\u003e, then that read \u003cem\u003ewould\u003c/em\u003e be assigned to the BC01 bin.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eBy default, Porechop only requires a single barcode match to bin a read. If you use the \u003ccode\u003e--require_two_barcodes\u003c/code\u003e option, then it will be much more stringent and assess the start and end of the read independently. I.e. to be binned, the start of a read must have a good match for a barcode and the end of the read must also have a good match for the same barcode. This will result in far more reads failing to be assigned to a bin, but the reads which are assigned have a very high confidence. Note that for some library preps (e.g. the rapid barcoding kit), barcodes may only be at the start of reads, in which case the \u003ccode\u003e--require_two_barcodes\u003c/code\u003e option is not appropriate.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eNote that the \u003ccode\u003e--discard_middle\u003c/code\u003e option is always active when demultiplexing barcoded reads. This is because a read with a middle adapter is likely chimeric and the pieces of chimeric reads may belong in separate bins.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eUsage examples:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003cstrong\u003eDefault settings\u003c/strong\u003e:\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz -b output_dir\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eStringent binning\u003c/strong\u003e (more reads in \"none\" bin but low risk of misclassified reads):\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz -b output_dir --barcode_threshold 85 --require_two_barcodes\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eLenient binning\u003c/strong\u003e (fewer reads in \"none\" bin but higher risk of misclassification):\u003cbr\u003e\n\u003ccode\u003eporechop -i input_reads.fastq.gz -b output_dir --barcode_threshold 60 --barcode_diff 1\u003c/code\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eBarcode demultiplexing with Albacore\u003c/h3\u003e\u003ca id=\"user-content-barcode-demultiplexing-with-albacore\" class=\"anchor\" aria-label=\"Permalink: Barcode demultiplexing with Albacore\" href=\"#barcode-demultiplexing-with-albacore\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e'What about Albacore's barcode demultiplexing?' I hear you say. 'Does this make Porechop's demultiplexing redundant?' Yes, Albacore v1.0 and later can demultiplex Nanopore reads during basecalling, which is a very nice feature. But Albacore and Porechop sometimes disagree on the appropriate bin for a read.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eSo if you use Albacore's output directory as input, here's what Porechop will do:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eLoad reads from all FASTQ files it finds, noting for each read what Albacore's bin was.\u003c/li\u003e\n\u003cli\u003eCall a barcode for each read using its normal demultiplexing logic.\u003c/li\u003e\n\u003cli\u003eTake all reads where Porechop and Albacore disagree and put them in the 'none' bin.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eFor example, Albacore may have put reads into the \u003ccode\u003ebarcode02\u003c/code\u003e directory. When Porechop trims and bins these reads, it may put 95% of them in the BC02 bin, but 4% go in the 'none' bin and 1% go into bins for other barcodes. By keeping only the 95% of reads where Albacore and Porechop agree, the risk of misclassification is reduced.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eOutput\u003c/h3\u003e\u003ca id=\"user-content-output\" class=\"anchor\" aria-label=\"Permalink: Output\" href=\"#output\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf Porechop is run with the output file specified using \u003ccode\u003e-o\u003c/code\u003e, it will display progress info to stdout. It will try to deduce the format of the output reads using the output filename (can handle \u003ccode\u003e.fastq\u003c/code\u003e, \u003ccode\u003e.fastq.gz\u003c/code\u003e, \u003ccode\u003e.fasta\u003c/code\u003e and \u003ccode\u003e.fasta.gz\u003c/code\u003e). The \u003ccode\u003e--format\u003c/code\u003e option can be used to override this automatic detection.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eAlternately, you can run Porechop with \u003ccode\u003e-b\u003c/code\u003e which specifies a directory for barcode bins. Porechop will then make separate read files in this directory for each barcode sequence (see \u003ca href=\"#barcode-demultiplexing\"\u003eBarcode demultiplexing\u003c/a\u003e for more details on the process). The files will be named using the barcode name or \"none\" if no barcode call was made (e.g. \u003ccode\u003eBC01.fastq.gz\u003c/code\u003e, \u003ccode\u003eBC02.fastq.gz\u003c/code\u003e, \u003ccode\u003enone.fastq.gz\u003c/code\u003e). The reads will be outputted in either \u003ccode\u003efasta\u003c/code\u003e, \u003ccode\u003efastq\u003c/code\u003e, \u003ccode\u003efasta.gz\u003c/code\u003e or \u003ccode\u003efastq.gz\u003c/code\u003e format, as determined by the input read format or the \u003ccode\u003e--format\u003c/code\u003e option.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eIf Porechop is run without \u003ccode\u003e-o\u003c/code\u003e or \u003ccode\u003e-b\u003c/code\u003e, then it will output the trimmed reads to stdout and print its progress info to stderr. The output format of the reads will be FASTA/FASTQ based on the input reads, or else can be specified using \u003ccode\u003e--format\u003c/code\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThe \u003ccode\u003e--verbosity\u003c/code\u003e option will change the amount of progress info:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003e\u003ccode\u003e--verbosity 0\u003c/code\u003e gives no progress output.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--verbosity 1\u003c/code\u003e (default) gives summary info about end adapter trimming and middle adapter splitting.\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--verbosity 2\u003c/code\u003e shows the actual trimmed/split sequences for each read (described more below).\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003e--verbosity 3\u003c/code\u003e shows tons of data (mainly for debugging).\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eVerbose output\u003c/h3\u003e\u003ca id=\"user-content-verbose-output\" class=\"anchor\" aria-label=\"Permalink: Verbose output\" href=\"#verbose-output\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eIf you call Porechop with \u003ccode\u003e--verbosity 2\u003c/code\u003e, then it will display the start/end of each read show the trimming in colour. Red indicates the adapter sequence and yellow indicates additional trimmed bases:\u003c/p\u003e\n\u003cp align=\"center\" dir=\"auto\"\u003e\u003ca target=\"_blank\" rel=\"noopener noreferrer\" href=\"/rrwick/Porechop/blob/master/misc/end_trimming.png\"\u003e\u003cimg src=\"/rrwick/Porechop/raw/master/misc/end_trimming.png\" alt=\"End trimming\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eIf you are \u003ca href=\"#barcode-demultiplexing\"\u003edemultiplexing barcodes\u003c/a\u003e, then this output will also show the barcodes found at the start/end of each read, along with the final call for the read's bin:\u003c/p\u003e\n\u003cp align=\"center\" dir=\"auto\"\u003e\u003ca target=\"_blank\" rel=\"noopener noreferrer\" href=\"/rrwick/Porechop/blob/master/misc/verbose_barcodes.png\"\u003e\u003cimg src=\"/rrwick/Porechop/raw/master/misc/verbose_barcodes.png\" alt=\"Barcodes\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThe same colour scheme is used for middle adapters, but only reads with a positive hit are displayed:\u003c/p\u003e\n\u003cp align=\"center\" dir=\"auto\"\u003e\u003ca target=\"_blank\" rel=\"noopener noreferrer\" href=\"/rrwick/Porechop/blob/master/misc/middle_adapters.png\"\u003e\u003cimg src=\"/rrwick/Porechop/raw/master/misc/middle_adapters.png\" alt=\"Middle adapters\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eKnown adapters\u003c/h1\u003e\u003ca id=\"user-content-known-adapters\" class=\"anchor\" aria-label=\"Permalink: Known adapters\" href=\"#known-adapters\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eThe known Nanopore adapters that Porechop looks for are defined in the \u003ca href=\"/rrwick/Porechop/blob/master/porechop/adapters.py\"\u003eadapters.py\u003c/a\u003e file.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThey are:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eLigation kit adapters\u003c/li\u003e\n\u003cli\u003eRapid kit adapters\u003c/li\u003e\n\u003cli\u003ePCR kit adapters\u003c/li\u003e\n\u003cli\u003eBarcodes\u003c/li\u003e\n\u003cli\u003eNative barcoding\u003c/li\u003e\n\u003cli\u003eRapid barcoding\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eIf you want to add your own adapter sequences to Porechop, you can do so by editing the \u003ca href=\"/rrwick/Porechop/blob/master/porechop/adapters.py\"\u003eadapters.py\u003c/a\u003e file (instructions are in that file). And if you know of any adapter sequences that I've missed, please let me know and I'll add them!\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eFull usage\u003c/h1\u003e\u003ca id=\"user-content-full-usage\" class=\"anchor\" aria-label=\"Permalink: Full usage\" href=\"#full-usage\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"snippet-clipboard-content notranslate position-relative overflow-auto\" data-snippet-clipboard-copy-content=\"usage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]\n [-t THREADS] [-b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD]\n [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] [--untrimmed]\n [--discard_unassigned] [--adapter_threshold ADAPTER_THRESHOLD]\n [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] [--end_size END_SIZE]\n [--min_trim_size MIN_TRIM_SIZE] [--extra_end_trim EXTRA_END_TRIM]\n [--end_threshold END_THRESHOLD] [--no_split] [--discard_middle]\n [--middle_threshold MIDDLE_THRESHOLD]\n [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE]\n [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE]\n [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version]\n\nPorechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and\nsplitting reads with internal adapters\n\nMain options:\n -i INPUT, --input INPUT FASTA/FASTQ of input reads or a directory which will be\n recursively searched for FASTQ files (required)\n -o OUTPUT, --output OUTPUT Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed\n reads will be printed to stdout)\n --format {auto,fasta,fastq,fasta.gz,fastq.gz}\n Output format for the reads - if auto, the format will be chosen\n based on the output filename or the input read format (default:\n auto)\n -v VERBOSITY, --verbosity VERBOSITY\n Level of progress information: 0 = none, 1 = some, 2 = lots, 3 =\n full - output will go to stdout if reads are saved to a file and\n stderr if reads are printed to stdout (default: 1)\n -t THREADS, --threads THREADS Number of threads to use for adapter alignment (default: 8)\n\nBarcode binning settings:\n Control the binning of reads based on barcodes (i.e. barcode demultiplexing)\n\n -b BARCODE_DIR, --barcode_dir BARCODE_DIR\n Reads will be binned based on their barcode and saved to separate\n files in this directory (incompatible with --output)\n --barcode_threshold BARCODE_THRESHOLD\n A read must have at least this percent identity to a barcode to be\n binned (default: 75.0)\n --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its\n second-best barcode identity is less than this value, it will not\n be put in a barcode bin (to exclude cases which are too close to\n call) (default: 5.0)\n --require_two_barcodes Reads will only be put in barcode bins if they have a strong match\n for the barcode on both their start and end (default: a read can\n be binned with a match at its start or end)\n --untrimmed Bin reads but do not trim them (default: trim the reads)\n --discard_unassigned Discard unassigned reads (instead of creating a \u0026quot;none\u0026quot; bin)\n (default: False)\n\nAdapter search settings:\n Control how the program determines which adapter sets are present\n\n --adapter_threshold ADAPTER_THRESHOLD\n An adapter set has to have at least this percent identity to be\n labelled as present and trimmed off (0 to 100) (default: 90.0)\n --check_reads CHECK_READS This many reads will be aligned to all possible adapters to\n determine which adapter sets are present (default: 10000)\n --scoring_scheme SCORING_SCHEME\n Comma-delimited string of alignment scores: match, mismatch, gap\n open, gap extend (default: 3,-6,-5,-2)\n\nEnd adapter settings:\n Control the trimming of adapters from read ends\n\n --end_size END_SIZE The number of base pairs at each end of the read which will be\n searched for adapter sequences (default: 150)\n --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4)\n --extra_end_trim EXTRA_END_TRIM\n This many additional bases will be removed next to adapters found\n at the ends of reads (default: 2)\n --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent\n identity to be removed (0 to 100) (default: 75.0)\n\nMiddle adapter settings:\n Control the splitting of read from middle adapters\n\n --no_split Skip splitting reads based on middle adapters (default: split\n reads when an adapter is found in the middle)\n --discard_middle Reads with middle adapters will be discarded (default: reads with\n middle adapters are split) (required for reads to be used with\n Nanopolish, this option is on by default when outputting reads\n into barcode bins)\n --middle_threshold MIDDLE_THRESHOLD\n Adapters in the middle of reads must have at least this percent\n identity to be found (0 to 100) (default: 85.0)\n --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE\n This many additional bases will be removed next to middle adapters\n on their \u0026quot;good\u0026quot; side (default: 10)\n --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE\n This many additional bases will be removed next to middle adapters\n on their \u0026quot;bad\u0026quot; side (default: 100)\n --min_split_read_size MIN_SPLIT_READ_SIZE\n Post-split read pieces smaller than this many base pairs will not\n be outputted (default: 1000)\n\nHelp:\n -h, --help Show this help message and exit\n --version Show program's version number and exit\"\u003e\u003cpre class=\"notranslate\"\u003e\u003ccode\u003eusage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]\n [-t THREADS] [-b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD]\n [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] [--untrimmed]\n [--discard_unassigned] [--adapter_threshold ADAPTER_THRESHOLD]\n [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] [--end_size END_SIZE]\n [--min_trim_size MIN_TRIM_SIZE] [--extra_end_trim EXTRA_END_TRIM]\n [--end_threshold END_THRESHOLD] [--no_split] [--discard_middle]\n [--middle_threshold MIDDLE_THRESHOLD]\n [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE]\n [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE]\n [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version]\n\nPorechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and\nsplitting reads with internal adapters\n\nMain options:\n -i INPUT, --input INPUT FASTA/FASTQ of input reads or a directory which will be\n recursively searched for FASTQ files (required)\n -o OUTPUT, --output OUTPUT Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed\n reads will be printed to stdout)\n --format {auto,fasta,fastq,fasta.gz,fastq.gz}\n Output format for the reads - if auto, the format will be chosen\n based on the output filename or the input read format (default:\n auto)\n -v VERBOSITY, --verbosity VERBOSITY\n Level of progress information: 0 = none, 1 = some, 2 = lots, 3 =\n full - output will go to stdout if reads are saved to a file and\n stderr if reads are printed to stdout (default: 1)\n -t THREADS, --threads THREADS Number of threads to use for adapter alignment (default: 8)\n\nBarcode binning settings:\n Control the binning of reads based on barcodes (i.e. barcode demultiplexing)\n\n -b BARCODE_DIR, --barcode_dir BARCODE_DIR\n Reads will be binned based on their barcode and saved to separate\n files in this directory (incompatible with --output)\n --barcode_threshold BARCODE_THRESHOLD\n A read must have at least this percent identity to a barcode to be\n binned (default: 75.0)\n --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its\n second-best barcode identity is less than this value, it will not\n be put in a barcode bin (to exclude cases which are too close to\n call) (default: 5.0)\n --require_two_barcodes Reads will only be put in barcode bins if they have a strong match\n for the barcode on both their start and end (default: a read can\n be binned with a match at its start or end)\n --untrimmed Bin reads but do not trim them (default: trim the reads)\n --discard_unassigned Discard unassigned reads (instead of creating a \"none\" bin)\n (default: False)\n\nAdapter search settings:\n Control how the program determines which adapter sets are present\n\n --adapter_threshold ADAPTER_THRESHOLD\n An adapter set has to have at least this percent identity to be\n labelled as present and trimmed off (0 to 100) (default: 90.0)\n --check_reads CHECK_READS This many reads will be aligned to all possible adapters to\n determine which adapter sets are present (default: 10000)\n --scoring_scheme SCORING_SCHEME\n Comma-delimited string of alignment scores: match, mismatch, gap\n open, gap extend (default: 3,-6,-5,-2)\n\nEnd adapter settings:\n Control the trimming of adapters from read ends\n\n --end_size END_SIZE The number of base pairs at each end of the read which will be\n searched for adapter sequences (default: 150)\n --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4)\n --extra_end_trim EXTRA_END_TRIM\n This many additional bases will be removed next to adapters found\n at the ends of reads (default: 2)\n --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent\n identity to be removed (0 to 100) (default: 75.0)\n\nMiddle adapter settings:\n Control the splitting of read from middle adapters\n\n --no_split Skip splitting reads based on middle adapters (default: split\n reads when an adapter is found in the middle)\n --discard_middle Reads with middle adapters will be discarded (default: reads with\n middle adapters are split) (required for reads to be used with\n Nanopolish, this option is on by default when outputting reads\n into barcode bins)\n --middle_threshold MIDDLE_THRESHOLD\n Adapters in the middle of reads must have at least this percent\n identity to be found (0 to 100) (default: 85.0)\n --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE\n This many additional bases will be removed next to middle adapters\n on their \"good\" side (default: 10)\n --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE\n This many additional bases will be removed next to middle adapters\n on their \"bad\" side (default: 100)\n --min_split_read_size MIN_SPLIT_READ_SIZE\n Post-split read pieces smaller than this many base pairs will not\n be outputted (default: 1000)\n\nHelp:\n -h, --help Show this help message and exit\n --version Show program's version number and exit\n\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eKnown issues\u003c/h1\u003e\u003ca id=\"user-content-known-issues\" class=\"anchor\" aria-label=\"Permalink: Known issues\" href=\"#known-issues\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eAdapter search\u003c/h3\u003e\u003ca id=\"user-content-adapter-search\" class=\"anchor\" aria-label=\"Permalink: Adapter search\" href=\"#adapter-search\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003ePorechop tries to automatically determine which adapters are present by looking at the reads, but this approach has a few issues:\u003c/p\u003e\n\u003cul dir=\"auto\"\u003e\n\u003cli\u003eAs the number of kits/barcodes has grown, adapter-search part of the Porechop's pipeline has become increasingly slow.\u003c/li\u003e\n\u003cli\u003ePorechop only does the adapter search on a subset of reads, which means there can be problems with non-randomly ordered read sets (e.g. all barcode 1 reads at the start of a file, followed by barcode 2 reads, etc).\u003c/li\u003e\n\u003cli\u003eMany ONT adapters share common sequence with each other, making false positive adapter finds possible.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp dir=\"auto\"\u003eA simpler solution (and in hindsight what I should have done) would be to require the kit and/or adapters from the user. E.g. \u003ccode\u003eporechop --sqk-lsk109\u003c/code\u003e or \u003ccode\u003eporechop --start_adapt ACGCTAGCATACGT\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003ePerformance\u003c/h3\u003e\u003ca id=\"user-content-performance\" class=\"anchor\" aria-label=\"Permalink: Performance\" href=\"#performance\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003ePorechop uses \u003ca href=\"https://github.com/seqan/seqan\"\u003eSeqAn\u003c/a\u003e to perform its alignments in C++. This library is very flexible, but not as fast as some alternatives, such as \u003ca href=\"https://github.com/Martinsos/edlib\"\u003eEdlib\u003c/a\u003e.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eAnother performance issue is that Porechop uses \u003ca href=\"https://docs.python.org/3/library/ctypes.html\" rel=\"nofollow\"\u003ectypes\u003c/a\u003e to interface with its C++ code. Function calls with ctypes can have a bit of overhead, which means that Porechop cannot use threads very efficiently (it spends too much of its time in the Python code, which is intrinsically non-parallel).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eBarcode demultiplexing\u003c/h3\u003e\u003ca id=\"user-content-barcode-demultiplexing-1\" class=\"anchor\" aria-label=\"Permalink: Barcode demultiplexing\" href=\"#barcode-demultiplexing-1\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eI added demultiplexing to Porechop as an afterthought – it was already looking for barcodes to trim, so why not sort reads by barcodes too? This turned out to be a very useful feature, but in hindsight I think it might be simpler (and easier to maintain) if trimming and demultiplexing functionality were in separate tools.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch3 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eBase-space problems\u003c/h3\u003e\u003ca id=\"user-content-base-space-problems\" class=\"anchor\" aria-label=\"Permalink: Base-space problems\" href=\"#base-space-problems\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003eI've encountered a couple of issues where adapter sequences are not properly basecalled, resulting in inconsistent sequence. Porechop trims in base-space, so this is a somewhat intractable problem. See \u003ca href=\"https://github.com/rrwick/Porechop/issues/40\" data-hovercard-type=\"issue\" data-hovercard-url=\"/rrwick/Porechop/issues/40/hovercard\"\u003eissue #40\u003c/a\u003e for an example.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eThese have made me wonder if the adapter trimming should be done in signal-space instead, though that would be a more complex problem to solve. I hope that in the future ONT can integrate this kind of functionality directly into their basecallers.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eAcknowledgements\u003c/h1\u003e\u003ca id=\"user-content-acknowledgements\" class=\"anchor\" aria-label=\"Permalink: Acknowledgements\" href=\"#acknowledgements\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003ePorechop was inspired by (and largely coded during) \u003ca href=\"https://porecamp-au.github.io/\" rel=\"nofollow\"\u003ePorecamp Australia 2017\u003c/a\u003e. Thanks to the organisers and attendees who helped me realise that a Nanopore adapter trimmer might be a useful tool! I later met David Stoddart from Oxford Nanopore at London Calling 2017, and he helped me get many of the adapter sequences right.\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eAlso I'd like to thank the \u003ca href=\"https://www.seqan.de/\" rel=\"nofollow\"\u003eSeqAn\u003c/a\u003e developers for their great library (Porechop uses SeqAn to perform its alignments).\u003c/p\u003e\n\u003cp dir=\"auto\"\u003eAnd of course, many thanks to \u003ca href=\"https://holtlab.net/\" rel=\"nofollow\"\u003eKat Holt\u003c/a\u003e and \u003ca href=\"https://scholar.google.com.au/citations?user=eO22mYUAAAAJ\u0026amp;hl=en\" rel=\"nofollow\"\u003eLouise Judd\u003c/a\u003e for keeping me well supplied with Nanopore reads!\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\" dir=\"auto\"\u003e\u003ch1 tabindex=\"-1\" class=\"heading-element\" dir=\"auto\"\u003eLicense\u003c/h1\u003e\u003ca id=\"user-content-license\" class=\"anchor\" aria-label=\"Permalink: License\" href=\"#license\"\u003e\u003csvg class=\"octicon octicon-link\" viewBox=\"0 0 16 16\" version=\"1.1\" width=\"16\" height=\"16\" aria-hidden=\"true\"\u003e\u003cpath d=\"m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z\"\u003e\u003c/path\u003e\u003c/svg\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp dir=\"auto\"\u003e\u003ca href=\"https://www.gnu.org/licenses/gpl-3.0.html\" rel=\"nofollow\"\u003eGNU General Public License, version 3\u003c/a\u003e\u003c/p\u003e\n\u003c/article\u003e","loaded":true,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":[{"level":3,"text":"Oct 2018 update: Porechop is officially unsupported","anchor":"oct-2018-update-porechop-is-officially-unsupported","htmlText":"Oct 2018 update: Porechop is officially unsupported"},{"level":1,"text":"Table of contents","anchor":"table-of-contents","htmlText":"Table of contents"},{"level":1,"text":"Requirements","anchor":"requirements","htmlText":"Requirements"},{"level":1,"text":"Installation","anchor":"installation","htmlText":"Installation"},{"level":3,"text":"Install from source","anchor":"install-from-source","htmlText":"Install from source"},{"level":3,"text":"Build and run without installation","anchor":"build-and-run-without-installation","htmlText":"Build and run without installation"},{"level":1,"text":"Quick usage examples","anchor":"quick-usage-examples","htmlText":"Quick usage examples"},{"level":1,"text":"How it works","anchor":"how-it-works","htmlText":"How it works"},{"level":3,"text":"Find matching adapter sets","anchor":"find-matching-adapter-sets","htmlText":"Find matching adapter sets"},{"level":3,"text":"Trim adapters from read ends","anchor":"trim-adapters-from-read-ends","htmlText":"Trim adapters from read ends"},{"level":3,"text":"Split reads with internal adapters","anchor":"split-reads-with-internal-adapters","htmlText":"Split reads with internal adapters"},{"level":3,"text":"Discard reads with internal adapters","anchor":"discard-reads-with-internal-adapters","htmlText":"Discard reads with internal adapters"},{"level":3,"text":"Barcode demultiplexing","anchor":"barcode-demultiplexing","htmlText":"Barcode demultiplexing"},{"level":3,"text":"Barcode demultiplexing with Albacore","anchor":"barcode-demultiplexing-with-albacore","htmlText":"Barcode demultiplexing with Albacore"},{"level":3,"text":"Output","anchor":"output","htmlText":"Output"},{"level":3,"text":"Verbose output","anchor":"verbose-output","htmlText":"Verbose output"},{"level":1,"text":"Known adapters","anchor":"known-adapters","htmlText":"Known adapters"},{"level":1,"text":"Full usage","anchor":"full-usage","htmlText":"Full usage"},{"level":1,"text":"Known issues","anchor":"known-issues","htmlText":"Known issues"},{"level":3,"text":"Adapter search","anchor":"adapter-search","htmlText":"Adapter search"},{"level":3,"text":"Performance","anchor":"performance","htmlText":"Performance"},{"level":3,"text":"Barcode demultiplexing","anchor":"barcode-demultiplexing-1","htmlText":"Barcode demultiplexing"},{"level":3,"text":"Base-space problems","anchor":"base-space-problems","htmlText":"Base-space problems"},{"level":1,"text":"Acknowledgements","anchor":"acknowledgements","htmlText":"Acknowledgements"},{"level":1,"text":"License","anchor":"license","htmlText":"License"}],"siteNavLoginPath":"/login?return_to=https%3A%2F%2Fgithub.com%2Frrwick%2FPorechop"}},{"displayName":"LICENSE","repoName":"Porechop","refName":"master","path":"LICENSE","preferredFileType":"license","tabName":"GPL-3.0","richText":null,"loaded":false,"timedOut":false,"errorMessage":null,"headerInfo":{"toc":null,"siteNavLoginPath":"/login?return_to=https%3A%2F%2Fgithub.com%2Frrwick%2FPorechop"}}],"overviewFilesProcessingTime":0}},"appPayload":{"helpUrl":"https://docs.github.com","findFileWorkerPath":"/assets-cdn/worker/find-file-worker-1583894afd38.js","findInFileWorkerPath":"/assets-cdn/worker/find-in-file-worker-67668e8c2caa.js","githubDevUrl":null,"enabled_features":{"code_nav_ui_events":false,"overview_shared_code_dropdown_button":false,"react_blob_overlay":false,"copilot_conversational_ux_embedding_update":false,"copilot_smell_icebreaker_ux":true,"copilot_workspace":false,"blob_edit_unsaved_changes_storage":true,"accessible_code_button":true}}}}</script> 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viewBox="0 0 16 16" width="16" height="16" fill="currentColor" style="display:inline-block;user-select:none;vertical-align:text-bottom;overflow:visible"><path d="m4.427 7.427 3.396 3.396a.25.25 0 0 0 .354 0l3.396-3.396A.25.25 0 0 0 11.396 7H4.604a.25.25 0 0 0-.177.427Z"></path></svg></span></span></button><div class="Box-sc-g0xbh4-0 izFOf"><button data-component="IconButton" type="button" aria-label="Open more actions menu" aria-haspopup="true" aria-expanded="false" tabindex="0" class="types__StyledButton-sc-ws60qy-0 gGdPyq prc-Button-IconButton-szpyj" data-loading="false" data-no-visuals="true" data-size="medium" aria-describedby=":R75ab:-loading-announcement" id=":R75ab:"><svg aria-hidden="true" focusable="false" class="octicon octicon-kebab-horizontal" viewBox="0 0 16 16" width="16" height="16" fill="currentColor" style="display:inline-block;user-select:none;vertical-align:text-bottom;overflow:visible"><path d="M8 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3ZM1.5 9a1.5 1.5 0 1 0 0-3 1.5 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aria-describedby=":Raqj8pab:-loading-announcement"><span data-component="buttonContent" class="Box-sc-g0xbh4-0 gUkoLg"><span data-component="leadingVisual" class="Box-sc-g0xbh4-0 hzSPyu"><svg aria-hidden="true" focusable="false" class="octicon octicon-history" viewBox="0 0 16 16" width="16" height="16" fill="currentColor" style="display:inline-block;user-select:none;vertical-align:text-bottom;overflow:visible"><path d="m.427 1.927 1.215 1.215a8.002 8.002 0 1 1-1.6 5.685.75.75 0 1 1 1.493-.154 6.5 6.5 0 1 0 1.18-4.458l1.358 1.358A.25.25 0 0 1 3.896 6H.25A.25.25 0 0 1 0 5.75V2.104a.25.25 0 0 1 .427-.177ZM7.75 4a.75.75 0 0 1 .75.75v2.992l2.028.812a.75.75 0 0 1-.557 1.392l-2.5-1A.751.751 0 0 1 7 8.25v-3.5A.75.75 0 0 1 7.75 4Z"></path></svg></span><span data-component="text"><span class="fgColor-default">115 Commits</span></span></span></a><div class="d-sm-none"></div><div class="d-flex d-lg-none"><span role="tooltip" aria-label="115 Commits" id="history-icon-button-tooltip" 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7 8.25v-3.5A.75.75 0 0 1 7.75 4Z"></path></svg></span></span></a></span></div></div></div></div></td></tr><tr class="react-directory-row undefined" id="folder-row-0"><td class="react-directory-row-name-cell-small-screen" colSpan="2"><div class="react-directory-filename-column"><svg aria-hidden="true" focusable="false" class="icon-directory" viewBox="0 0 16 16" width="16" height="16" fill="currentColor" style="display:inline-block;user-select:none;vertical-align:text-bottom;overflow:visible"><path d="M1.75 1A1.75 1.75 0 0 0 0 2.75v10.5C0 14.216.784 15 1.75 15h12.5A1.75 1.75 0 0 0 16 13.25v-8.5A1.75 1.75 0 0 0 14.25 3H7.5a.25.25 0 0 1-.2-.1l-.9-1.2C6.07 1.26 5.55 1 5 1H1.75Z"></path></svg><div class="overflow-hidden"><div class="react-directory-filename-cell"><div class="react-directory-truncate"><a title="misc" aria-label="misc, (Directory)" class="Link--primary" href="/rrwick/Porechop/tree/master/misc">misc</a></div></div></div></div></td><td 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1.75 15h12.5A1.75 1.75 0 0 0 16 13.25v-8.5A1.75 1.75 0 0 0 14.25 3H7.5a.25.25 0 0 1-.2-.1l-.9-1.2C6.07 1.26 5.55 1 5 1H1.75Z"></path></svg><div class="overflow-hidden"><div class="react-directory-filename-cell"><div class="react-directory-truncate"><a title="test" aria-label="test, (Directory)" class="Link--primary" href="/rrwick/Porechop/tree/master/test">test</a></div></div></div></div></td><td class="react-directory-row-commit-cell"><div class="Skeleton Skeleton--text"> </div></td><td><div class="Skeleton Skeleton--text"> </div></td></tr><tr class="react-directory-row undefined" id="folder-row-3"><td class="react-directory-row-name-cell-small-screen" colSpan="2"><div class="react-directory-filename-column"><svg aria-hidden="true" focusable="false" class="color-fg-muted" viewBox="0 0 16 16" width="16" height="16" fill="currentColor" style="display:inline-block;user-select:none;vertical-align:text-bottom;overflow:visible"><path d="M2 1.75C2 .784 2.784 0 3.75 0h6.586c.464 0 .909.184 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2.914c.329.328.513.773.513 1.237v9.586A1.75 1.75 0 0 1 13.25 16h-9.5A1.75 1.75 0 0 1 2 14.25Zm1.75-.25a.25.25 0 0 0-.25.25v12.5c0 .138.112.25.25.25h9.5a.25.25 0 0 0 .25-.25V6h-2.75A1.75 1.75 0 0 1 9 4.25V1.5Zm6.75.062V4.25c0 .138.112.25.25.25h2.688l-.011-.013-2.914-2.914-.013-.011Z"></path></svg><div class="overflow-hidden"><div class="react-directory-filename-cell"><div class="react-directory-truncate"><a title=".gitignore" aria-label=".gitignore, (File)" class="Link--primary" href="/rrwick/Porechop/blob/master/.gitignore">.gitignore</a></div></div></div></div></td><td class="react-directory-row-commit-cell"><div class="Skeleton Skeleton--text"> </div></td><td><div class="Skeleton Skeleton--text"> </div></td></tr><tr class="react-directory-row undefined" id="folder-row-4"><td class="react-directory-row-name-cell-small-screen" colSpan="2"><div class="react-directory-filename-column"><svg aria-hidden="true" focusable="false" class="color-fg-muted" viewBox="0 0 16 16" width="16" 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2.5h8.5a.75.75 0 0 1 0 1.5h-8.5a.75.75 0 0 1 0-1.5Zm0 5h8.5a.75.75 0 0 1 0 1.5h-8.5a.75.75 0 0 1 0-1.5Zm0 5h8.5a.75.75 0 0 1 0 1.5h-8.5a.75.75 0 0 1 0-1.5ZM2 14a1 1 0 1 1 0-2 1 1 0 0 1 0 2Zm1-6a1 1 0 1 1-2 0 1 1 0 0 1 2 0ZM2 4a1 1 0 1 1 0-2 1 1 0 0 1 0 2Z"></path></svg></button></div><div class="Box-sc-g0xbh4-0 QkQOb js-snippet-clipboard-copy-unpositioned" data-hpc="true"><article class="markdown-body entry-content container-lg" itemprop="text"><p align="center" dir="auto"><a target="_blank" rel="noopener noreferrer" href="/rrwick/Porechop/blob/master/misc/porechop_logo_knife.png"><img src="/rrwick/Porechop/raw/master/misc/porechop_logo_knife.png" alt="Porechop" width="600" style="max-width: 100%;"></a></p> <p dir="auto">Porechop is a tool for finding and removing adapters from <a href="https://nanoporetech.com/" rel="nofollow">Oxford Nanopore</a> reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.</p> <p dir="auto">Porechop also supports demultiplexing of Nanopore reads that were barcoded with the <a href="https://store.nanoporetech.com/native-barcoding-kit-1d.html" rel="nofollow">Native Barcoding Kit</a>, <a href="https://store.nanoporetech.com/pcr-barcoding-kit-96.html" rel="nofollow">PCR Barcoding Kit</a> or <a href="https://store.nanoporetech.com/rapid-barcoding-sequencing-kit.html" rel="nofollow">Rapid Barcoding Kit</a>.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Oct 2018 update: Porechop is officially unsupported</h3><a id="user-content-oct-2018-update-porechop-is-officially-unsupported" class="anchor" aria-label="Permalink: Oct 2018 update: Porechop is officially unsupported" href="#oct-2018-update-porechop-is-officially-unsupported"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">While I'm happy Porechop has so many users, it has always been a bit klugey and a pain to maintain. I don't have the time to give it the attention it deserves, so I'm going to now officially declare Porechop as abandonware (though the unanswered <a href="https://github.com/rrwick/Porechop/issues">issues</a> and <a href="https://github.com/rrwick/Porechop/pulls">pull requests</a> reveal that it already has been for some time). I've added a <a href="#known-issues">known issues</a> section to the README to outline what I think is wrong with Porechop and how a reimplementation should look. I may someday (no promises though 😛) try to rewrite it from a blank canvas to address its faults.</p> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Table of contents</h1><a id="user-content-table-of-contents" class="anchor" aria-label="Permalink: Table of contents" href="#table-of-contents"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li><a href="#requirements">Requirements</a></li> <li><a href="#installation">Installation</a> <ul dir="auto"> <li><a href="#install-from-source">Install from source</a></li> <li><a href="#build-and-run-without-installation">Build and run without installation</a></li> </ul> </li> <li><a href="#quick-usage-examples">Quick usage examples</a></li> <li><a href="#how-it-works">How it works</a> <ul dir="auto"> <li><a href="#find-matching-adapter-sets">Find matching adapter sets</a></li> <li><a href="#trim-adapters-from-read-ends">Trim adapters from read ends</a></li> <li><a href="#split-reads-with-internal-adapters">Split reads with internal adapters</a></li> <li><a href="#discard-reads-with-internal-adapters">Discard reads with internal adapters</a></li> <li><a href="#barcode-demultiplexing">Barcode demultiplexing</a></li> <li><a href="#barcode-demultiplexing-with-albacore">Barcode demultiplexing with Albacore</a></li> <li><a href="#output">Output</a></li> <li><a href="#verbose-output">Verbose output</a></li> </ul> </li> <li><a href="#known-adapters">Known adapters</a></li> <li><a href="#full-usage">Full usage</a></li> <li><a href="#known-issues">Known issues</a></li> <li><a href="#acknowledgements">Acknowledgements</a></li> <li><a href="#license">License</a></li> </ul> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Requirements</h1><a id="user-content-requirements" class="anchor" aria-label="Permalink: Requirements" href="#requirements"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <ul dir="auto"> <li>Linux or macOS</li> <li><a href="https://www.python.org/" rel="nofollow">Python</a> 3.4 or later</li> <li>C++ compiler <ul dir="auto"> <li>If you're using <a href="https://gcc.gnu.org/" rel="nofollow">GCC</a>, version 4.9.1 or later is required (check with <code>g++ --version</code>).</li> <li>Recent versions of <a href="http://clang.llvm.org/" rel="nofollow">Clang</a> and <a href="https://software.intel.com/en-us/c-compilers" rel="nofollow">ICC</a> should also work (C++14 support is required).</li> </ul> </li> </ul> <p dir="auto">I haven't tried to make Porechop run on Windows, but it should be possible. If you have any success on this front, let me know and I'll add instructions to this README!</p> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Installation</h1><a id="user-content-installation" class="anchor" aria-label="Permalink: Installation" href="#installation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Install from source</h3><a id="user-content-install-from-source" class="anchor" aria-label="Permalink: Install from source" href="#install-from-source"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Running the <code>setup.py</code> script will compile the C++ components of Porechop and install a <code>porechop</code> executable:</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="git clone https://github.com/rrwick/Porechop.git cd Porechop python3 setup.py install porechop -h"><pre>git clone https://github.com/rrwick/Porechop.git <span class="pl-c1">cd</span> Porechop python3 setup.py install porechop -h</pre></div> <p dir="auto">Notes:</p> <ul dir="auto"> <li>If the last command complains about permissions, you may need to run it with <code>sudo</code>.</li> <li>Install just for your user: <code>python3 setup.py install --user</code> <ul dir="auto"> <li>If you get a strange "can't combine user with prefix" error, read <a href="http://stackoverflow.com/questions/4495120" rel="nofollow">this</a>.</li> </ul> </li> <li>Install to a specific location: <code>python3 setup.py install --prefix=$HOME/.local</code></li> <li>Install with pip (local copy): <code>pip3 install path/to/Porechop</code></li> <li>Install with pip (from GitHub): <code>pip3 install git+https://github.com/rrwick/Porechop.git</code></li> <li>If you'd like to specify which compiler to use, set the <code>CXX</code> variable: <code>export CXX=g++-6; python3 setup.py install</code></li> <li>Porechop includes <code>ez_setup.py</code> for users who don't have <a href="https://pypi.python.org/pypi/setuptools" rel="nofollow">setuptools</a> installed, though that script is <a href="https://github.com/pypa/setuptools/issues/581" data-hovercard-type="issue" data-hovercard-url="/pypa/setuptools/issues/581/hovercard">deprecated</a>. So if you run into any installation problems, make sure setuptools is installed on your computer: <code>pip3 install setuptools</code></li> </ul> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Build and run without installation</h3><a id="user-content-build-and-run-without-installation" class="anchor" aria-label="Permalink: Build and run without installation" href="#build-and-run-without-installation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">By simply running <code>make</code> in Porechop's directory, you can compile the C++ components but not install an executable. The program can then be executed by directly calling the <code>porechop-runner.py</code> script.</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="git clone https://github.com/rrwick/Porechop.git cd Porechop make ./porechop-runner.py -h"><pre>git clone https://github.com/rrwick/Porechop.git <span class="pl-c1">cd</span> Porechop make ./porechop-runner.py -h</pre></div> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Quick usage examples</h1><a id="user-content-quick-usage-examples" class="anchor" aria-label="Permalink: Quick usage examples" href="#quick-usage-examples"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto"><strong>Basic adapter trimming:</strong><br> <code>porechop -i input_reads.fastq.gz -o output_reads.fastq.gz</code></p> <p dir="auto"><strong>Trimmed reads to stdout, if you prefer:</strong><br> <code>porechop -i input_reads.fastq.gz > output_reads.fastq</code></p> <p dir="auto"><strong>Demultiplex barcoded reads:</strong><br> <code>porechop -i input_reads.fastq.gz -b output_dir</code></p> <p dir="auto"><strong>Demultiplex barcoded reads, straight from Albacore output directory:</strong><br> <code>porechop -i albacore_dir -b output_dir</code></p> <p dir="auto"><strong>Also works with FASTA:</strong><br> <code>porechop -i input_reads.fasta -o output_reads.fasta</code></p> <p dir="auto"><strong>More verbose output:</strong><br> <code>porechop -i input_reads.fastq.gz -o output_reads.fastq.gz --verbosity 2</code></p> <p dir="auto"><strong>Got a big server?</strong><br> <code>porechop -i input_reads.fastq.gz -o output_reads.fastq.gz --threads 40</code></p> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">How it works</h1><a id="user-content-how-it-works" class="anchor" aria-label="Permalink: How it works" href="#how-it-works"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Find matching adapter sets</h3><a id="user-content-find-matching-adapter-sets" class="anchor" aria-label="Permalink: Find matching adapter sets" href="#find-matching-adapter-sets"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Porechop first aligns a subset of reads (default 10000 reads, change with <code>--check_reads</code>) to all known adapter sets. Adapter sets with at least one high identity match (default 90%, change with <code>--adapter_threshold</code>) are deemed present in the sample.</p> <p dir="auto">Identity in this step is measured over the full length of the adapter. E.g. in order to qualify for a 90% match, an adapter could be present at 90% identity over its full length, or it could be present at 100% identity over 90% of its length, but a 90% identity match over 90% of the adapter length would not be sufficient.</p> <p dir="auto">The <a href="http://seqan.readthedocs.io/en/master/Tutorial/DataStructures/Alignment/ScoringSchemes.html" rel="nofollow">alignment scoring scheme</a> used in this and subsequent alignments can be modified using the <code>--scoring_scheme</code> option (default: match = 3, mismatch = -6, gap open = -5, gap extend = -2).</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Trim adapters from read ends</h3><a id="user-content-trim-adapters-from-read-ends" class="anchor" aria-label="Permalink: Trim adapters from read ends" href="#trim-adapters-from-read-ends"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The first and last bases in each read (default 150 bases, change with <code>--end_size</code>) are aligned to each present adapter set. When a long enough (default 4, change with <code>--min_trim_size</code>) and strong enough (default 75%, change with <code>--end_threshold</code>) match is found, the read is trimmed. A few extra bases (default 2, change with <code>--extra_end_trim</code>) past the adapter match are removed as well to ensure it's all removed.</p> <p dir="auto">Identity in this step is measured over the <em>aligned part</em> of the adapter, not its full length. E.g. if the last 5 bases of an adapter exactly match the first 5 bases of a read, that counts as a 100% identity match and those bases will be trimmed off. This allows Porechop to effectively trim partially present barcodes.</p> <p dir="auto">The default <code>--end_threshold</code> is low (75%) because false positives (trimming off some sequence that wasn't really an adapter) shouldn't be too much of a problem with long reads, as only a tiny fraction of the read is lost.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Split reads with internal adapters</h3><a id="user-content-split-reads-with-internal-adapters" class="anchor" aria-label="Permalink: Split reads with internal adapters" href="#split-reads-with-internal-adapters"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The entirety of each read is aligned to the present adapter sets to spot cases where an adapter is in the middle of the read, indicating a chimera. When a strong enough match is found (default 85%, change with <code>--middle_threshold</code>), the read is split. If the resulting parts are too short (default less than 1000 bp, change with <code>--min_split_read_size</code>), they are discarded.</p> <p dir="auto">The default <code>--middle_threshold</code> (85%) is higher than the default <code>--end_threshold</code> (75%) because false positives in this step (splitting a read that is not chimeric) could be more problematic than false positives in the end trimming step. If false negatives (failing to split a chimera) are worse for you than false positives (splitting a non-chimera), you should reduce this threshold (e.g. <code>--middle_threshold 75</code>).</p> <p dir="auto">Extra bases are also removed next to the hit, and how many depends on the side of the adapter. If we find an adapter that's expected at the start of a read, it's likely that what follows is good sequence but what precedes it may not be. Therefore, a few bases are trimmed after the adapter (default 10, change with <code>--extra_middle_trim_good_side</code>) and more bases are trimmed before the adapter (default 100, change with <code>--extra_middle_trim_bad_side</code>). If the found adapter is one we'd expect at the end of the read, then the "good side" is before the adapter and the "bad side" is after the adapter.</p> <p dir="auto">Here is a real example of the "good" and "bad" sides of an adapter. The adapter is in the middle of this snippet (SQK-NSK007_Y_Top at about 90% identity). The bases to the left are the "bad" side and their repetitive nature is clear. The bases to the right are the "good" side and represent real biological sequence.</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="TGTTGTTGTTGTTATTGTTGTTATTGTTGTTGTATTGTTGTTATTGTTGTTGTTGTACATTGTTATTGTTGTATTGTTGTTATTGTTGTTGTATTATCGGTGTACTTCGTTCAGTTACGTATTACTATCGCTATTGTTTGCAGTGAGAGGTGGCGGTGAGCGTTTTCAAATGGCCCTGTACAATCATGGGATAACAACATAAGGAACGGACCATGAAGTCACTTCT"><pre class="notranslate"><code>TGTTGTTGTTGTTATTGTTGTTATTGTTGTTGTATTGTTGTTATTGTTGTTGTTGTACATTGTTATTGTTGTATTGTTGTTATTGTTGTTGTATTATCGGTGTACTTCGTTCAGTTACGTATTACTATCGCTATTGTTTGCAGTGAGAGGTGGCGGTGAGCGTTTTCAAATGGCCCTGTACAATCATGGGATAACAACATAAGGAACGGACCATGAAGTCACTTCT </code></pre></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Discard reads with internal adapters</h3><a id="user-content-discard-reads-with-internal-adapters" class="anchor" aria-label="Permalink: Discard reads with internal adapters" href="#discard-reads-with-internal-adapters"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">If you run Porechop with <code>--discard_middle</code>, the reads with internal adapters will be thrown out instead of split.</p> <p dir="auto">If you plan on using your reads with <a href="https://github.com/jts/nanopolish">Nanopolish</a>, then the <code>--discard_middle</code> option is required. This is because Nanopolish first runs <a href="https://github.com/jts/nanopolish#data-preprocessing"><code>nanopolish index</code></a> to find a one-to-one association between FASTQ reads and fast5 files. If you ran Porechop <em>without</em> <code>--discard_middle</code>, then you could end up with multiple separate FASTQ reads which are from a single fast5, and this is incompatible with Nanopolish.</p> <p dir="auto">This option is also recommended if you are trimming reads from a demultiplexed barcoded sequencing run. This is because chimeric reads may contain two sequences from two separate barcodes, so throwing them out is the safer option to reduce cross-barcode contamination.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Barcode demultiplexing</h3><a id="user-content-barcode-demultiplexing" class="anchor" aria-label="Permalink: Barcode demultiplexing" href="#barcode-demultiplexing"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Porechop can also demultiplex the reads into bins based on which barcode was found. This is done by using the <code>-b</code> option, which specifies an output directory for the trimmed reads (each barcode in a separate file), instead of <code>-o</code>.</p> <p dir="auto">Porechop looks for barcodes at the start and end of each read. All barcode matches are found, and if the best match is strong enough (default 75%, change with <code>--barcode_threshold</code>) and sufficiently better than the second-best barcode match (default 5% better, change with <code>--barcode_diff</code>), then the read is assigned to that barcode bin. E.g. with default settings, if BC01 was found at 79% identity and BC02 was found at 76% identity, the read will not be assigned to a barcode bin because the results were too close. But if you used <code>--barcode_diff 1</code>, then that read <em>would</em> be assigned to the BC01 bin.</p> <p dir="auto">By default, Porechop only requires a single barcode match to bin a read. If you use the <code>--require_two_barcodes</code> option, then it will be much more stringent and assess the start and end of the read independently. I.e. to be binned, the start of a read must have a good match for a barcode and the end of the read must also have a good match for the same barcode. This will result in far more reads failing to be assigned to a bin, but the reads which are assigned have a very high confidence. Note that for some library preps (e.g. the rapid barcoding kit), barcodes may only be at the start of reads, in which case the <code>--require_two_barcodes</code> option is not appropriate.</p> <p dir="auto">Note that the <code>--discard_middle</code> option is always active when demultiplexing barcoded reads. This is because a read with a middle adapter is likely chimeric and the pieces of chimeric reads may belong in separate bins.</p> <p dir="auto">Usage examples:</p> <ul dir="auto"> <li><strong>Default settings</strong>:<br> <code>porechop -i input_reads.fastq.gz -b output_dir</code></li> <li><strong>Stringent binning</strong> (more reads in "none" bin but low risk of misclassified reads):<br> <code>porechop -i input_reads.fastq.gz -b output_dir --barcode_threshold 85 --require_two_barcodes</code></li> <li><strong>Lenient binning</strong> (fewer reads in "none" bin but higher risk of misclassification):<br> <code>porechop -i input_reads.fastq.gz -b output_dir --barcode_threshold 60 --barcode_diff 1</code></li> </ul> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Barcode demultiplexing with Albacore</h3><a id="user-content-barcode-demultiplexing-with-albacore" class="anchor" aria-label="Permalink: Barcode demultiplexing with Albacore" href="#barcode-demultiplexing-with-albacore"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">'What about Albacore's barcode demultiplexing?' I hear you say. 'Does this make Porechop's demultiplexing redundant?' Yes, Albacore v1.0 and later can demultiplex Nanopore reads during basecalling, which is a very nice feature. But Albacore and Porechop sometimes disagree on the appropriate bin for a read.</p> <p dir="auto">So if you use Albacore's output directory as input, here's what Porechop will do:</p> <ul dir="auto"> <li>Load reads from all FASTQ files it finds, noting for each read what Albacore's bin was.</li> <li>Call a barcode for each read using its normal demultiplexing logic.</li> <li>Take all reads where Porechop and Albacore disagree and put them in the 'none' bin.</li> </ul> <p dir="auto">For example, Albacore may have put reads into the <code>barcode02</code> directory. When Porechop trims and bins these reads, it may put 95% of them in the BC02 bin, but 4% go in the 'none' bin and 1% go into bins for other barcodes. By keeping only the 95% of reads where Albacore and Porechop agree, the risk of misclassification is reduced.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Output</h3><a id="user-content-output" class="anchor" aria-label="Permalink: Output" href="#output"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">If Porechop is run with the output file specified using <code>-o</code>, it will display progress info to stdout. It will try to deduce the format of the output reads using the output filename (can handle <code>.fastq</code>, <code>.fastq.gz</code>, <code>.fasta</code> and <code>.fasta.gz</code>). The <code>--format</code> option can be used to override this automatic detection.</p> <p dir="auto">Alternately, you can run Porechop with <code>-b</code> which specifies a directory for barcode bins. Porechop will then make separate read files in this directory for each barcode sequence (see <a href="#barcode-demultiplexing">Barcode demultiplexing</a> for more details on the process). The files will be named using the barcode name or "none" if no barcode call was made (e.g. <code>BC01.fastq.gz</code>, <code>BC02.fastq.gz</code>, <code>none.fastq.gz</code>). The reads will be outputted in either <code>fasta</code>, <code>fastq</code>, <code>fasta.gz</code> or <code>fastq.gz</code> format, as determined by the input read format or the <code>--format</code> option.</p> <p dir="auto">If Porechop is run without <code>-o</code> or <code>-b</code>, then it will output the trimmed reads to stdout and print its progress info to stderr. The output format of the reads will be FASTA/FASTQ based on the input reads, or else can be specified using <code>--format</code>.</p> <p dir="auto">The <code>--verbosity</code> option will change the amount of progress info:</p> <ul dir="auto"> <li><code>--verbosity 0</code> gives no progress output.</li> <li><code>--verbosity 1</code> (default) gives summary info about end adapter trimming and middle adapter splitting.</li> <li><code>--verbosity 2</code> shows the actual trimmed/split sequences for each read (described more below).</li> <li><code>--verbosity 3</code> shows tons of data (mainly for debugging).</li> </ul> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Verbose output</h3><a id="user-content-verbose-output" class="anchor" aria-label="Permalink: Verbose output" href="#verbose-output"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">If you call Porechop with <code>--verbosity 2</code>, then it will display the start/end of each read show the trimming in colour. Red indicates the adapter sequence and yellow indicates additional trimmed bases:</p> <p align="center" dir="auto"><a target="_blank" rel="noopener noreferrer" href="/rrwick/Porechop/blob/master/misc/end_trimming.png"><img src="/rrwick/Porechop/raw/master/misc/end_trimming.png" alt="End trimming" style="max-width: 100%;"></a></p> <p dir="auto">If you are <a href="#barcode-demultiplexing">demultiplexing barcodes</a>, then this output will also show the barcodes found at the start/end of each read, along with the final call for the read's bin:</p> <p align="center" dir="auto"><a target="_blank" rel="noopener noreferrer" href="/rrwick/Porechop/blob/master/misc/verbose_barcodes.png"><img src="/rrwick/Porechop/raw/master/misc/verbose_barcodes.png" alt="Barcodes" style="max-width: 100%;"></a></p> <p dir="auto">The same colour scheme is used for middle adapters, but only reads with a positive hit are displayed:</p> <p align="center" dir="auto"><a target="_blank" rel="noopener noreferrer" href="/rrwick/Porechop/blob/master/misc/middle_adapters.png"><img src="/rrwick/Porechop/raw/master/misc/middle_adapters.png" alt="Middle adapters" style="max-width: 100%;"></a></p> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Known adapters</h1><a id="user-content-known-adapters" class="anchor" aria-label="Permalink: Known adapters" href="#known-adapters"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">The known Nanopore adapters that Porechop looks for are defined in the <a href="/rrwick/Porechop/blob/master/porechop/adapters.py">adapters.py</a> file.</p> <p dir="auto">They are:</p> <ul dir="auto"> <li>Ligation kit adapters</li> <li>Rapid kit adapters</li> <li>PCR kit adapters</li> <li>Barcodes</li> <li>Native barcoding</li> <li>Rapid barcoding</li> </ul> <p dir="auto">If you want to add your own adapter sequences to Porechop, you can do so by editing the <a href="/rrwick/Porechop/blob/master/porechop/adapters.py">adapters.py</a> file (instructions are in that file). And if you know of any adapter sequences that I've missed, please let me know and I'll add them!</p> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Full usage</h1><a id="user-content-full-usage" class="anchor" aria-label="Permalink: Full usage" href="#full-usage"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="usage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] [-t THREADS] [-b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD] [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] [--untrimmed] [--discard_unassigned] [--adapter_threshold ADAPTER_THRESHOLD] [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE] [--extra_end_trim EXTRA_END_TRIM] [--end_threshold END_THRESHOLD] [--no_split] [--discard_middle] [--middle_threshold MIDDLE_THRESHOLD] [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE] [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE] [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version] Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and splitting reads with internal adapters Main options: -i INPUT, --input INPUT FASTA/FASTQ of input reads or a directory which will be recursively searched for FASTQ files (required) -o OUTPUT, --output OUTPUT Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed reads will be printed to stdout) --format {auto,fasta,fastq,fasta.gz,fastq.gz} Output format for the reads - if auto, the format will be chosen based on the output filename or the input read format (default: auto) -v VERBOSITY, --verbosity VERBOSITY Level of progress information: 0 = none, 1 = some, 2 = lots, 3 = full - output will go to stdout if reads are saved to a file and stderr if reads are printed to stdout (default: 1) -t THREADS, --threads THREADS Number of threads to use for adapter alignment (default: 8) Barcode binning settings: Control the binning of reads based on barcodes (i.e. barcode demultiplexing) -b BARCODE_DIR, --barcode_dir BARCODE_DIR Reads will be binned based on their barcode and saved to separate files in this directory (incompatible with --output) --barcode_threshold BARCODE_THRESHOLD A read must have at least this percent identity to a barcode to be binned (default: 75.0) --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its second-best barcode identity is less than this value, it will not be put in a barcode bin (to exclude cases which are too close to call) (default: 5.0) --require_two_barcodes Reads will only be put in barcode bins if they have a strong match for the barcode on both their start and end (default: a read can be binned with a match at its start or end) --untrimmed Bin reads but do not trim them (default: trim the reads) --discard_unassigned Discard unassigned reads (instead of creating a "none" bin) (default: False) Adapter search settings: Control how the program determines which adapter sets are present --adapter_threshold ADAPTER_THRESHOLD An adapter set has to have at least this percent identity to be labelled as present and trimmed off (0 to 100) (default: 90.0) --check_reads CHECK_READS This many reads will be aligned to all possible adapters to determine which adapter sets are present (default: 10000) --scoring_scheme SCORING_SCHEME Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default: 3,-6,-5,-2) End adapter settings: Control the trimming of adapters from read ends --end_size END_SIZE The number of base pairs at each end of the read which will be searched for adapter sequences (default: 150) --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4) --extra_end_trim EXTRA_END_TRIM This many additional bases will be removed next to adapters found at the ends of reads (default: 2) --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent identity to be removed (0 to 100) (default: 75.0) Middle adapter settings: Control the splitting of read from middle adapters --no_split Skip splitting reads based on middle adapters (default: split reads when an adapter is found in the middle) --discard_middle Reads with middle adapters will be discarded (default: reads with middle adapters are split) (required for reads to be used with Nanopolish, this option is on by default when outputting reads into barcode bins) --middle_threshold MIDDLE_THRESHOLD Adapters in the middle of reads must have at least this percent identity to be found (0 to 100) (default: 85.0) --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE This many additional bases will be removed next to middle adapters on their "good" side (default: 10) --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE This many additional bases will be removed next to middle adapters on their "bad" side (default: 100) --min_split_read_size MIN_SPLIT_READ_SIZE Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000) Help: -h, --help Show this help message and exit --version Show program's version number and exit"><pre class="notranslate"><code>usage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY] [-t THREADS] [-b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD] [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] [--untrimmed] [--discard_unassigned] [--adapter_threshold ADAPTER_THRESHOLD] [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE] [--extra_end_trim EXTRA_END_TRIM] [--end_threshold END_THRESHOLD] [--no_split] [--discard_middle] [--middle_threshold MIDDLE_THRESHOLD] [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE] [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE] [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version] Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and splitting reads with internal adapters Main options: -i INPUT, --input INPUT FASTA/FASTQ of input reads or a directory which will be recursively searched for FASTQ files (required) -o OUTPUT, --output OUTPUT Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed reads will be printed to stdout) --format {auto,fasta,fastq,fasta.gz,fastq.gz} Output format for the reads - if auto, the format will be chosen based on the output filename or the input read format (default: auto) -v VERBOSITY, --verbosity VERBOSITY Level of progress information: 0 = none, 1 = some, 2 = lots, 3 = full - output will go to stdout if reads are saved to a file and stderr if reads are printed to stdout (default: 1) -t THREADS, --threads THREADS Number of threads to use for adapter alignment (default: 8) Barcode binning settings: Control the binning of reads based on barcodes (i.e. barcode demultiplexing) -b BARCODE_DIR, --barcode_dir BARCODE_DIR Reads will be binned based on their barcode and saved to separate files in this directory (incompatible with --output) --barcode_threshold BARCODE_THRESHOLD A read must have at least this percent identity to a barcode to be binned (default: 75.0) --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its second-best barcode identity is less than this value, it will not be put in a barcode bin (to exclude cases which are too close to call) (default: 5.0) --require_two_barcodes Reads will only be put in barcode bins if they have a strong match for the barcode on both their start and end (default: a read can be binned with a match at its start or end) --untrimmed Bin reads but do not trim them (default: trim the reads) --discard_unassigned Discard unassigned reads (instead of creating a "none" bin) (default: False) Adapter search settings: Control how the program determines which adapter sets are present --adapter_threshold ADAPTER_THRESHOLD An adapter set has to have at least this percent identity to be labelled as present and trimmed off (0 to 100) (default: 90.0) --check_reads CHECK_READS This many reads will be aligned to all possible adapters to determine which adapter sets are present (default: 10000) --scoring_scheme SCORING_SCHEME Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default: 3,-6,-5,-2) End adapter settings: Control the trimming of adapters from read ends --end_size END_SIZE The number of base pairs at each end of the read which will be searched for adapter sequences (default: 150) --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4) --extra_end_trim EXTRA_END_TRIM This many additional bases will be removed next to adapters found at the ends of reads (default: 2) --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent identity to be removed (0 to 100) (default: 75.0) Middle adapter settings: Control the splitting of read from middle adapters --no_split Skip splitting reads based on middle adapters (default: split reads when an adapter is found in the middle) --discard_middle Reads with middle adapters will be discarded (default: reads with middle adapters are split) (required for reads to be used with Nanopolish, this option is on by default when outputting reads into barcode bins) --middle_threshold MIDDLE_THRESHOLD Adapters in the middle of reads must have at least this percent identity to be found (0 to 100) (default: 85.0) --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE This many additional bases will be removed next to middle adapters on their "good" side (default: 10) --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE This many additional bases will be removed next to middle adapters on their "bad" side (default: 100) --min_split_read_size MIN_SPLIT_READ_SIZE Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000) Help: -h, --help Show this help message and exit --version Show program's version number and exit </code></pre></div> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Known issues</h1><a id="user-content-known-issues" class="anchor" aria-label="Permalink: Known issues" href="#known-issues"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Adapter search</h3><a id="user-content-adapter-search" class="anchor" aria-label="Permalink: Adapter search" href="#adapter-search"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Porechop tries to automatically determine which adapters are present by looking at the reads, but this approach has a few issues:</p> <ul dir="auto"> <li>As the number of kits/barcodes has grown, adapter-search part of the Porechop's pipeline has become increasingly slow.</li> <li>Porechop only does the adapter search on a subset of reads, which means there can be problems with non-randomly ordered read sets (e.g. all barcode 1 reads at the start of a file, followed by barcode 2 reads, etc).</li> <li>Many ONT adapters share common sequence with each other, making false positive adapter finds possible.</li> </ul> <p dir="auto">A simpler solution (and in hindsight what I should have done) would be to require the kit and/or adapters from the user. E.g. <code>porechop --sqk-lsk109</code> or <code>porechop --start_adapt ACGCTAGCATACGT</code>.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Performance</h3><a id="user-content-performance" class="anchor" aria-label="Permalink: Performance" href="#performance"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Porechop uses <a href="https://github.com/seqan/seqan">SeqAn</a> to perform its alignments in C++. This library is very flexible, but not as fast as some alternatives, such as <a href="https://github.com/Martinsos/edlib">Edlib</a>.</p> <p dir="auto">Another performance issue is that Porechop uses <a href="https://docs.python.org/3/library/ctypes.html" rel="nofollow">ctypes</a> to interface with its C++ code. Function calls with ctypes can have a bit of overhead, which means that Porechop cannot use threads very efficiently (it spends too much of its time in the Python code, which is intrinsically non-parallel).</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Barcode demultiplexing</h3><a id="user-content-barcode-demultiplexing-1" class="anchor" aria-label="Permalink: Barcode demultiplexing" href="#barcode-demultiplexing-1"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">I added demultiplexing to Porechop as an afterthought – it was already looking for barcodes to trim, so why not sort reads by barcodes too? This turned out to be a very useful feature, but in hindsight I think it might be simpler (and easier to maintain) if trimming and demultiplexing functionality were in separate tools.</p> <div class="markdown-heading" dir="auto"><h3 tabindex="-1" class="heading-element" dir="auto">Base-space problems</h3><a id="user-content-base-space-problems" class="anchor" aria-label="Permalink: Base-space problems" href="#base-space-problems"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">I've encountered a couple of issues where adapter sequences are not properly basecalled, resulting in inconsistent sequence. Porechop trims in base-space, so this is a somewhat intractable problem. See <a href="https://github.com/rrwick/Porechop/issues/40" data-hovercard-type="issue" data-hovercard-url="/rrwick/Porechop/issues/40/hovercard">issue #40</a> for an example.</p> <p dir="auto">These have made me wonder if the adapter trimming should be done in signal-space instead, though that would be a more complex problem to solve. I hope that in the future ONT can integrate this kind of functionality directly into their basecallers.</p> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">Acknowledgements</h1><a id="user-content-acknowledgements" class="anchor" aria-label="Permalink: Acknowledgements" href="#acknowledgements"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018 1.998 1.998 0 0 0 2.83 0l2.5-2.5a2.002 2.002 0 0 0-2.83-2.83l-1.25 1.25a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042Zm-4.69 9.64a1.998 1.998 0 0 0 2.83 0l1.25-1.25a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042l-1.25 1.25a3.5 3.5 0 1 1-4.95-4.95l2.5-2.5a3.5 3.5 0 0 1 4.95 0 .751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018 1.998 1.998 0 0 0-2.83 0l-2.5 2.5a1.998 1.998 0 0 0 0 2.83Z"></path></svg></a></div> <p dir="auto">Porechop was inspired by (and largely coded during) <a href="https://porecamp-au.github.io/" rel="nofollow">Porecamp Australia 2017</a>. Thanks to the organisers and attendees who helped me realise that a Nanopore adapter trimmer might be a useful tool! I later met David Stoddart from Oxford Nanopore at London Calling 2017, and he helped me get many of the adapter sequences right.</p> <p dir="auto">Also I'd like to thank the <a href="https://www.seqan.de/" rel="nofollow">SeqAn</a> developers for their great library (Porechop uses SeqAn to perform its alignments).</p> <p dir="auto">And of course, many thanks to <a href="https://holtlab.net/" rel="nofollow">Kat Holt</a> and <a href="https://scholar.google.com.au/citations?user=eO22mYUAAAAJ&hl=en" rel="nofollow">Louise Judd</a> for keeping me well supplied with Nanopore reads!</p> <div class="markdown-heading" dir="auto"><h1 tabindex="-1" class="heading-element" dir="auto">License</h1><a id="user-content-license" class="anchor" aria-label="Permalink: License" href="#license"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path d="m7.775 3.275 1.25-1.25a3.5 3.5 0 1 1 4.95 4.95l-2.5 2.5a3.5 3.5 0 0 1-4.95 0 .751.751 0 0 1 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