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id="block-bccrc-breadcrumbs" class="block block--system-breadcrumb-block block-bccrc-breadcrumbs"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">GSC</a> </li> <li> <a href="/resources">Resources</a> </li> <li> Software </li> </ol> </nav> </section> <section id="block-bccrc-page-title" class="block block--page-title-block block-bccrc-page-title"> <h1><span property="schema:name">Software</span> </h1> </section> </div> </header> <section class="region region__highlight"> <div class="region__highlight--inner region--inner"> <div data-drupal-messages-fallback class="hidden"></div> </div> </section> <main role="main"> <a id="main-content" tabindex="-1"></a> <div class="layout-content"> <section class="region region__content"> <div class="region__content--inner region--inner"> <section id="block-bccrc-content" class="block block--system-main-block block-bccrc-content"> <article role="article" about="/resources/software" typeof="schema:WebPage" class="node node--page full"> <span property="schema:name" content="Software" class="hidden"></span> <div property="schema:text" class="field field--body"><p>The rapid evolution of DNA sequencing technologies over the past 20 years has made it possible to generate enormous amounts of data, and has subsequently spurred the development of computational tools needed to assemble complete genomes and to analyze genomic, transcriptomic and proteomic data. The GSC collaborates with and supports research by the wider research community. We have聽an extensive collection of software packages developed in-house available for download here and through GitHub.</p></div> </article> <section class="layout layout__expanding layout__parent__node paragraph paragraph--type--expanding paragraph--view-mode--default" id="paragraph--301"> <div class="field field--field_expanding_logo"> <img src="/sites/default/files/2019-12/github-logo_1.png" width="362" height="112" alt="GitHub Logo" typeof="foaf:Image" /> </div> <div class="field field--field_expanding_summary"><a href="https://github.com/bcgsc/">https://github.com/bcgsc/</a></div> </section> </section> <section class="views-element-container block block--views-blocksoftware-block-1 block-views-block-software-block-1" id="block-views-block-software-block-1"> <div><div class="js-view-dom-id-b6d92462c1d11640679c20b5eea94a61cdd62d2dac220d98e0505c56db730f74 view view--software"> <div class="views-view-grid view--software cols-3"> <article role="article" about="/resources/software/abyss" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/abyss" rel="bookmark" ><span>ABySS</span> </a> </h2> <div class="field field--body">Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/abyss" rel="tag" title="ABySS" hreflang="en">Learn more<span class="visually-hidden"> about ABySS</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/abyss-explorer" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/abyss-explorer" rel="bookmark" ><span>ABySS-Explorer</span> </a> </h2> <div class="field field--body">A sequence assembly visualization tool</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/abyss-explorer" rel="tag" title="ABySS-Explorer" hreflang="en">Learn more<span class="visually-hidden"> about ABySS-Explorer</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/adapter-trimming-for-small-rna-sequencing" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/adapter-trimming-for-small-rna-sequencing" rel="bookmark" ><span>Adapter Trimming for Small RNA Sequencing</span> </a> </h2> <div class="field field--body">Removes 3' adapter from Illumina sequencing of small RNAs where read length is greater than the size of RNAs</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/adapter-trimming-for-small-rna-sequencing" rel="tag" title="Adapter Trimming for Small RNA Sequencing" hreflang="en">Learn more<span class="visually-hidden"> about Adapter Trimming for Small RNA Sequencing</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/alea" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/alea" rel="bookmark" ><span>ALEA</span> </a> </h2> <div class="field field--body">ALEA is a computational toolbox for allele-specific (AS) epigenomics analysis</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/alea" rel="tag" title="ALEA" hreflang="en">Learn more<span class="visually-hidden"> about ALEA</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/amplify" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/amplify" rel="bookmark" ><span>AMPlify</span> </a> </h2> <div class="field field--body">Attentive deep learning model for antimicrobial peptide prediction</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/amplify" rel="tag" title="AMPlify" hreflang="en">Learn more<span class="visually-hidden"> about AMPlify</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/anchor" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/anchor" rel="bookmark" ><span>Anchor</span> </a> </h2> <div class="field field--body">Post-processing tools for de novo assemblies</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/anchor" rel="tag" title="Anchor" hreflang="en">Learn more<span class="visually-hidden"> about Anchor</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/arcs" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/arcs" rel="bookmark" ><span>ARCS/ARKS</span> </a> </h2> <div class="field field--body">Genome assembly scaffolder with linked and long reads</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/arcs" rel="tag" title="ARCS/ARKS" hreflang="en">Learn more<span class="visually-hidden"> about ARCS/ARKS</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/barnacle" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/barnacle" rel="bookmark" ><span>Barnacle</span> </a> </h2> <div class="field field--body">A pipeline for detecting and characterizing chimeric transcripts from long RNA sequences</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/barnacle" rel="tag" title="Barnacle" hreflang="en">Learn more<span class="visually-hidden"> about Barnacle</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/biobloomtools" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/biobloomtools" rel="bookmark" ><span>BioBloomTools</span> </a> </h2> <div class="field field--body">BioBloom Tools (BBT) is a general use fast sequence categorization tool utilizing Bloom filters</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/biobloomtools" rel="tag" title="BioBloomTools" hreflang="en">Learn more<span class="visually-hidden"> about BioBloomTools</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/bliss" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/bliss" rel="bookmark" ><span>BLISS</span> </a> </h2> <div class="field field--body">Batch anaLysIS Suite (BLISS)</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/bliss" rel="tag" title="BLISS" hreflang="en">Learn more<span class="visually-hidden"> about BLISS</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/btllib" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/btllib" rel="bookmark" ><span>btllib</span> </a> </h2> <div class="field field--body">A common code library with efficient code and wrappers for many common bioinformatics operations</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/btllib" rel="tag" title="btllib" hreflang="en">Learn more<span class="visually-hidden"> about btllib</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/chinook" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/chinook" rel="bookmark" ><span>Chinook</span> </a> </h2> <div class="field field--body">Chinook is a peer-to-peer (P2P) bioinformatics service</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/chinook" rel="tag" title="Chinook" hreflang="en">Learn more<span class="visually-hidden"> about Chinook</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/chopstitch" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/chopstitch" rel="bookmark" ><span>ChopStitch</span> </a> </h2> <div class="field field--body">Exon annotation and splice graph reconstruction using transcriptome assembly and whole genome sequencing data</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/chopstitch" rel="tag" title="ChopStitch" hreflang="en">Learn more<span class="visually-hidden"> about ChopStitch</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/circos" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/circos" rel="bookmark" ><span>Circos</span> </a> </h2> <div class="field field--body">Visualize comparative genomic data such as alignments, conservation, homology, synteny and other positional n-tuples in an attractive and informative circular layout</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/circos" rel="tag" title="Circos" hreflang="en">Learn more<span class="visually-hidden"> about Circos</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/coral" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/coral" rel="bookmark" ><span>CORAL</span> </a> </h2> <div class="field field--body">Contig Ordering Algorithm</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/coral" rel="tag" title="CORAL" hreflang="en">Learn more<span class="visually-hidden"> about CORAL</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/dida" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/dida" rel="bookmark" ><span>DIDA</span> </a> </h2> <div class="field field--body">DIDA is a novel framework that performs the large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/dida" rel="tag" title="DIDA" hreflang="en">Learn more<span class="visually-hidden"> about DIDA</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/discoveryspace" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/discoveryspace" rel="bookmark" ><span>DiscoverySpace</span> </a> </h2> <div class="field field--body">DiscoverySpace is a graphical software application that intends to free the biologist from the micro-level, syntactic detail of the underlying data structures to concentrate on the "big picture" and the meaning of experimental results</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/discoveryspace" rel="tag" title="DiscoverySpace" hreflang="en">Learn more<span class="visually-hidden"> about DiscoverySpace</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/fassi" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/fassi" rel="bookmark" ><span>FASSI</span> </a> </h2> <div class="field field--body">Fingerprint and Assembly Incorporation</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/fassi" rel="tag" title="FASSI" hreflang="en">Learn more<span class="visually-hidden"> about FASSI</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/findpeaks" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/findpeaks" rel="bookmark" ><span>FindPeaks</span> </a> </h2> <div class="field field--body">Findpeaks was developed to perform analysis of ChIP-Seq experiments</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/findpeaks" rel="tag" title="FindPeaks" hreflang="en">Learn more<span class="visually-hidden"> about FindPeaks</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/goldrush" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/goldrush" rel="bookmark" ><span>GoldRush</span> </a> </h2> <div class="field field--body">A linear time聽de novo聽long read assembler</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/goldrush" rel="tag" title="GoldRush" hreflang="en">Learn more<span class="visually-hidden"> about GoldRush</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/graphner" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/graphner" rel="bookmark" ><span>GraphNER</span> </a> </h2> <div class="field field--body">GraphNER is a named entity recognizer that uses graph propagation and improves BANNER and BANNER-ChemDNER systems. Data is available for gene mention detection task</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/graphner" rel="tag" title="GraphNER" hreflang="en">Learn more<span class="visually-hidden"> about GraphNER</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/hlaminer" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/hlaminer" rel="bookmark" ><span>HLAminer</span> </a> </h2> <div class="field field--body">Derivation of HLA class I and II predictions from shotgun sequence data sets</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/hlaminer" rel="tag" title="HLAminer" hreflang="en">Learn more<span class="visually-hidden"> about HLAminer</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ice" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ice" rel="bookmark" ><span>Internet Contig Explorer (iCE)</span> </a> </h2> <div class="field field--body">iCE is used for viewing fingerprint maps and associated data</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ice" rel="tag" title="Internet Contig Explorer (iCE)" hreflang="en">Learn more<span class="visually-hidden"> about Internet Contig Explorer (iCE)</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/jaguar" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/jaguar" rel="bookmark" ><span>JAGuaR</span> </a> </h2> <div class="field field--body">Junction Alignments to Genome for RNA-seq Reads</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/jaguar" rel="tag" title="JAGuaR" hreflang="en">Learn more<span class="visually-hidden"> about JAGuaR</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/kleat" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/kleat" rel="bookmark" ><span>KLEAT</span> </a> </h2> <div class="field field--body">c(K)LEavage site Analysis of Transcriptomes (KLEAT) identifies 3' UTR ends of transcripts in de novo RNA-Seq assemblies</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/kleat" rel="tag" title="KLEAT" hreflang="en">Learn more<span class="visually-hidden"> about KLEAT</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/kollector" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/kollector" rel="bookmark" ><span>Kollector</span> </a> </h2> <div class="field field--body">Targeted de novo assembler</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/kollector" rel="tag" title="Kollector" hreflang="en">Learn more<span class="visually-hidden"> about Kollector</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/konnector" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/konnector" rel="bookmark" ><span>Konnector</span> </a> </h2> <div class="field field--body">Connecting Paired-end Reads Using a Bloom Filter de Bruijn Graph</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/konnector" rel="tag" title="Konnector" hreflang="en">Learn more<span class="visually-hidden"> about Konnector</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/laneruler" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/laneruler" rel="bookmark" ><span>LaneRuler</span> </a> </h2> <div class="field field--body">LaneRuler will identify lanes in a gel image. The core module is a command line C program, whose result can be reviewed and corrected using a Java interface</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/laneruler" rel="tag" title="LaneRuler" hreflang="en">Learn more<span class="visually-hidden"> about LaneRuler</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/links" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/links" rel="bookmark" ><span>LINKS</span> </a> </h2> <div class="field field--body">Long Interval Nucleotide K-mer Scaffolder</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/links" rel="tag" title="LINKS" hreflang="en">Learn more<span class="visually-hidden"> about LINKS</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/longstitch" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/longstitch" rel="bookmark" ><span>LongStitch</span> </a> </h2> <div class="field field--body">LongStitch is a聽de novo聽genome assembly correction and scaffolding pipeline. LongStitch聽runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long).</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/longstitch" rel="tag" title="LongStitch" hreflang="en">Learn more<span class="visually-hidden"> about LongStitch</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/mavis" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/mavis" rel="bookmark" ><span>MAVIS</span> </a> </h2> <div class="field field--body">A Python command-line tool for the post-processing of structural variant calls</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/mavis" rel="tag" title="MAVIS" hreflang="en">Learn more<span class="visually-hidden"> about MAVIS</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/mirna-profiling" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/mirna-profiling" rel="bookmark" ><span>MiRNA Profiling</span> </a> </h2> <div class="field field--body">Profile the content of a miRNA sequencing run</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/mirna-profiling" rel="tag" title="MiRNA Profiling" hreflang="en">Learn more<span class="visually-hidden"> about MiRNA Profiling</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/msss" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/msss" rel="bookmark" ><span>MSSS</span> </a> </h2> <div class="field field--body">Sampling with Minimum Sum of Squared Similarities for Nystrom-Based Large Scale Spectral Clustering Publication</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/msss" rel="tag" title="MSSS" hreflang="en">Learn more<span class="visually-hidden"> about MSSS</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/nanosim" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/nanosim" rel="bookmark" ><span>NanoSim</span> </a> </h2> <div class="field field--body">Nanopore sequence read simulator based on statistical characterization</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/nanosim" rel="tag" title="NanoSim" hreflang="en">Learn more<span class="visually-hidden"> about NanoSim</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ntcard" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ntcard" rel="bookmark" ><span>ntCard</span> </a> </h2> <div class="field field--body">ntCard: a streaming algorithm for cardinality estimation in genomics data</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ntcard" rel="tag" title="ntCard" hreflang="en">Learn more<span class="visually-hidden"> about ntCard</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ntedit" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ntedit" rel="bookmark" ><span>ntEdit</span> </a> </h2> <div class="field field--body">Scalable genome sequence polishing</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ntedit" rel="tag" title="ntEdit" hreflang="en">Learn more<span class="visually-hidden"> about ntEdit</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/nthash" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/nthash" rel="bookmark" ><span>ntHash</span> </a> </h2> <div class="field field--body">ntHash: recursive nucleotide hashing</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/nthash" rel="tag" title="ntHash" hreflang="en">Learn more<span class="visually-hidden"> about ntHash</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ntjoin" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ntjoin" rel="bookmark" ><span>ntJoin</span> </a> </h2> <div class="field field--body">Fast and lightweight assembly-guided scaffolding using minimizer graphs</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ntjoin" rel="tag" title="ntJoin" hreflang="en">Learn more<span class="visually-hidden"> about ntJoin</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ntlink" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ntlink" rel="bookmark" ><span>ntLink</span> </a> </h2> <div class="field field--body">ntLink is a lightweight聽de novo聽genome assembly scaffolder using long reads and minimizers.</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ntlink" rel="tag" title="ntLink" hreflang="en">Learn more<span class="visually-hidden"> about ntLink</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ntroot" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ntroot" rel="bookmark" ><span>ntRoot</span> </a> </h2> <div class="field field--body">ntRoot is an alignment-free, computationally lightweight method for inferring human super-population-level global and local ancestry from whole genome assemblies or raw sequencing data types.</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ntroot" rel="tag" title="ntRoot" hreflang="en">Learn more<span class="visually-hidden"> about ntRoot</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ntsynt" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ntsynt" rel="bookmark" ><span>ntSynt</span> </a> </h2> <div class="field field--body">ntSynt detects multi-genome synteny blocks using minimizer graph mappings.</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ntsynt" rel="tag" title="ntSynt" hreflang="en">Learn more<span class="visually-hidden"> about ntSynt</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/oreganno" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/oreganno" rel="bookmark" ><span>ORegAnno</span> </a> </h2> <div class="field field--body">Open Regulatory Annotation</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/oreganno" rel="tag" title="ORegAnno" hreflang="en">Learn more<span class="visually-hidden"> about ORegAnno</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/passit" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/passit" rel="bookmark" ><span>PASsiT</span> </a> </h2> <div class="field field--body">Post Alignment SNV Tools</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/passit" rel="tag" title="PASsiT" hreflang="en">Learn more<span class="visually-hidden"> about PASsiT</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/pavfinder" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/pavfinder" rel="bookmark" ><span>PAVFinder</span> </a> </h2> <div class="field field--body">Post-Assembly Variant Finder (PAVFinder) - Structural variant caller on sequence assembly</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/pavfinder" rel="tag" title="PAVFinder" hreflang="en">Learn more<span class="visually-hidden"> about PAVFinder</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/pavfinder_transcriptome" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/pavfinder_transcriptome" rel="bookmark" ><span>PAVFinder_transcriptome</span> </a> </h2> <div class="field field--body">Structural and splice variant detection from transcriptome assembly</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/pavfinder_transcriptome" rel="tag" title="PAVFinder_transcriptome" hreflang="en">Learn more<span class="visually-hidden"> about PAVFinder_transcriptome</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/physlr" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/physlr" rel="bookmark" ><span>Physlr</span> </a> </h2> <div class="field field--body">Constructing a physical map from linked reads. The physical map can then be used to scaffold draft genome assemblies</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/physlr" rel="tag" title="Physlr" hreflang="en">Learn more<span class="visually-hidden"> about Physlr</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/raw-quant" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/raw-quant" rel="bookmark" ><span>Raw Quant</span> </a> </h2> <div class="field field--body">A Python package for extracting scan meta data and quantification values from Thermo .raw files</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/raw-quant" rel="tag" title="Raw Quant" hreflang="en">Learn more<span class="visually-hidden"> about Raw Quant</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/rna-bloom" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/rna-bloom" rel="bookmark" ><span>RNA-Bloom</span> </a> </h2> <div class="field field--body">Reference-free transcriptome assembly for short and long reads</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/rna-bloom" rel="tag" title="RNA-Bloom" hreflang="en">Learn more<span class="visually-hidden"> about RNA-Bloom</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/sam" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/sam" rel="bookmark" ><span>SAM - Sequence Assembly Manager</span> </a> </h2> <div class="field field--body">SAM is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/sam" rel="tag" title="SAM - Sequence Assembly Manager" hreflang="en">Learn more<span class="visually-hidden"> about SAM - Sequence Assembly Manager</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/satellog" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/satellog" rel="bookmark" ><span>Satellog</span> </a> </h2> <div class="field field--body">A database for the identification and prioritization of satellite repeats in disease association studies</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/satellog" rel="tag" title="Satellog" hreflang="en">Learn more<span class="visually-hidden"> about Satellog</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/sealer" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/sealer" rel="bookmark" ><span>Sealer</span> </a> </h2> <div class="field field--body">Scalable gap-filler for finishing large genomes</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/sealer" rel="tag" title="Sealer" hreflang="en">Learn more<span class="visually-hidden"> about Sealer</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/slider" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/slider" rel="bookmark" ><span>Slider</span> </a> </h2> <div class="field field--body">Maximum use of probability information for alignment of short sequence reads and SNP detection</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/slider" rel="tag" title="Slider" hreflang="en">Learn more<span class="visually-hidden"> about Slider</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/sliderii" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/sliderii" rel="bookmark" ><span>SliderII</span> </a> </h2> <div class="field field--body">High quality SNP calling using Illumina data at minimal coverage</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/sliderii" rel="tag" title="SliderII" hreflang="en">Learn more<span class="visually-hidden"> about SliderII</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/snvmix" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/snvmix" rel="bookmark" ><span>SNVMix</span> </a> </h2> <div class="field field--body">Detecting single nucleotide variants from next generation sequencing data</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/snvmix" rel="tag" title="SNVMix" hreflang="en">Learn more<span class="visually-hidden"> about SNVMix</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/sockeye" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/sockeye" rel="bookmark" ><span>Sockeye</span> </a> </h2> <div class="field field--body">Genome visualization application</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/sockeye" rel="tag" title="Sockeye" hreflang="en">Learn more<span class="visually-hidden"> about Sockeye</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/spark" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/spark" rel="bookmark" ><span>Spark</span> </a> </h2> <div class="field field--body">NOTE: This software is now being distributed via <a href="http://www.sparkinsight.org">www.sparkinsight.org</a> - please see that site for the latest release</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/spark" rel="tag" title="Spark" hreflang="en">Learn more<span class="visually-hidden"> about Spark</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/ssake" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/ssake" rel="bookmark" ><span>SSAKE</span> </a> </h2> <div class="field field--body">De novo genome assembly with short DNA sequence reads</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/ssake" rel="tag" title="SSAKE" hreflang="en">Learn more<span class="visually-hidden"> about SSAKE</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/straglr" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/straglr" rel="bookmark" ><span>Straglr</span> </a> </h2> <div class="field field--body">Short-tandem repeat genotyping using long reads</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/straglr" rel="tag" title="Straglr" hreflang="en">Learn more<span class="visually-hidden"> about Straglr</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/tasr" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/tasr" rel="bookmark" ><span>TASR</span> </a> </h2> <div class="field field--body">Targeted Assembler of Short Sequence Reads</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/tasr" rel="tag" title="TASR" hreflang="en">Learn more<span class="visually-hidden"> about TASR</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/thor" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/thor" rel="bookmark" ><span>THOR</span> </a> </h2> <div class="field field--body">THOR, the Targeted High-throughput Ortholog Reconstructor, is a Java application designed to assemble target genomic sequence orthologs in low-coverage genomes</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/thor" rel="tag" title="THOR" hreflang="en">Learn more<span class="visually-hidden"> about THOR</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/tigmint" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/tigmint" rel="bookmark" ><span>Tigmint</span> </a> </h2> <div class="field field--body">Correct misassemblies in genome assembly drafts using linked or long DNA sequencing reads</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/tigmint" rel="tag" title="Tigmint" hreflang="en">Learn more<span class="visually-hidden"> about Tigmint</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/trans-abyss" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/trans-abyss" rel="bookmark" ><span>Trans-ABySS</span> </a> </h2> <div class="field field--body">de novo assembly of RNA-Seq data using ABySS</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/trans-abyss" rel="tag" title="Trans-ABySS" hreflang="en">Learn more<span class="visually-hidden"> about Trans-ABySS</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/treebuilder" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/treebuilder" rel="bookmark" ><span>TreeBuilder3D</span> </a> </h2> <div class="field field--body">TreeBuilder3D is an interactive viewer that allows the organization of SAGE and other types of gene expression data into hierarchical dendrograms, or phenetic networks</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/treebuilder" rel="tag" title="TreeBuilder3D" hreflang="en">Learn more<span class="visually-hidden"> about TreeBuilder3D</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/unikseq" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/unikseq" rel="bookmark" ><span>unikseq</span> </a> </h2> <div class="field field--body">Unique DNA sequence region identification, using a k-mer approach</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/unikseq" rel="tag" title="unikseq" hreflang="en">Learn more<span class="visually-hidden"> about unikseq</span></a></li></ul> </div> </article> <article role="article" about="/resources/software/xmatchview" class="node node--software teaser"> <div class="node__inner"> <h2 class="node__title"> <a href="/resources/software/xmatchview" rel="bookmark" ><span>XMatchView</span> </a> </h2> <div class="field field--body">XMatchView is a python application designed to visualize DNA sequence alignments</div> <ul class="links inline"><li class="node-readmore"><a href="/resources/software/xmatchview" rel="tag" title="XMatchView" hreflang="en">Learn more<span class="visually-hidden"> about XMatchView</span></a></li></ul> </div> </article> </div> </div> </div> </section> </div> </section> </div> <a class="top" href="#main-content">Back to top</a> </main> <footer class="page" role="contentinfo"> <section class="region region__footer"> <div class="region__footer--inner region--inner"> <section id="block-phsalogo" class="block 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