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<button aria-controls="toc-Variations-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Variations subsection</span> </button> <ul id="toc-Variations-sublist" class="vector-toc-list"> <li id="toc-Quality" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Quality"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.1</span> <span>Quality</span> </div> </a> <ul id="toc-Quality-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Encoding" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Encoding"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.2</span> <span>Encoding</span> </div> </a> <ul id="toc-Encoding-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Color_space" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Color_space"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.3</span> <span>Color space</span> </div> </a> <ul id="toc-Color_space-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-FAST5_and_HDF5_evolutions" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#FAST5_and_HDF5_evolutions"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.4</span> <span>FAST5 and HDF5 evolutions</span> </div> </a> <ul id="toc-FAST5_and_HDF5_evolutions-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Simulation" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Simulation"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.5</span> <span>Simulation</span> </div> </a> <ul id="toc-Simulation-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Compression" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Compression"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.6</span> <span>Compression</span> </div> </a> <ul id="toc-Compression-sublist" class="vector-toc-list"> <li id="toc-General_compressors" class="vector-toc-list-item vector-toc-level-3"> <a class="vector-toc-link" href="#General_compressors"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.6.1</span> <span>General compressors</span> </div> </a> <ul id="toc-General_compressors-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Reads" class="vector-toc-list-item vector-toc-level-3"> <a class="vector-toc-link" href="#Reads"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.6.2</span> <span>Reads</span> </div> </a> <ul id="toc-Reads-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Quality_values" class="vector-toc-list-item vector-toc-level-3"> <a class="vector-toc-link" href="#Quality_values"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.6.3</span> <span>Quality values</span> </div> </a> <ul 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<span>See also</span> </div> </a> <ul id="toc-See_also-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">6</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-External_links" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#External_links"> <div class="vector-toc-text"> <span class="vector-toc-numb">7</span> <span>External links</span> </div> </a> <ul id="toc-External_links-sublist" class="vector-toc-list"> </ul> </li> </ul> </div> </div> </nav> </div> </div> <div class="mw-content-container"> <main id="content" class="mw-body"> <header class="mw-body-header vector-page-titlebar"> <nav aria-label="Contents" class="vector-toc-landmark"> <div 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mw-first-heading"><span class="mw-page-title-main">FASTQ format</span></h1> <div id="p-lang-btn" class="vector-dropdown mw-portlet mw-portlet-lang" > <input type="checkbox" id="p-lang-btn-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-p-lang-btn" class="vector-dropdown-checkbox mw-interlanguage-selector" aria-label="Go to an article in another language. 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title="FASTQ – Czech" lang="cs" hreflang="cs" data-title="FASTQ" data-language-autonym="Čeština" data-language-local-name="Czech" class="interlanguage-link-target"><span>Čeština</span></a></li><li class="interlanguage-link interwiki-de mw-list-item"><a href="https://de.wikipedia.org/wiki/FASTQ-Format" title="FASTQ-Format – German" lang="de" hreflang="de" data-title="FASTQ-Format" data-language-autonym="Deutsch" data-language-local-name="German" class="interlanguage-link-target"><span>Deutsch</span></a></li><li class="interlanguage-link interwiki-et mw-list-item"><a href="https://et.wikipedia.org/wiki/FASTQ_formaat" title="FASTQ formaat – Estonian" lang="et" hreflang="et" data-title="FASTQ formaat" data-language-autonym="Eesti" data-language-local-name="Estonian" class="interlanguage-link-target"><span>Eesti</span></a></li><li class="interlanguage-link interwiki-es mw-list-item"><a href="https://es.wikipedia.org/wiki/Formato_FASTQ" title="Formato FASTQ – Spanish" lang="es" hreflang="es" data-title="Formato FASTQ" data-language-autonym="Español" data-language-local-name="Spanish" class="interlanguage-link-target"><span>Español</span></a></li><li class="interlanguage-link interwiki-fa mw-list-item"><a href="https://fa.wikipedia.org/wiki/%D9%82%D8%A7%D9%84%D8%A8_%D9%81%D8%B3%D8%AA%DA%A9" title="قالب فستک – Persian" lang="fa" hreflang="fa" data-title="قالب فستک" data-language-autonym="فارسی" data-language-local-name="Persian" class="interlanguage-link-target"><span>فارسی</span></a></li><li class="interlanguage-link interwiki-fr mw-list-item"><a href="https://fr.wikipedia.org/wiki/FASTQ" title="FASTQ – French" lang="fr" hreflang="fr" data-title="FASTQ" data-language-autonym="Français" data-language-local-name="French" class="interlanguage-link-target"><span>Français</span></a></li><li class="interlanguage-link interwiki-id mw-list-item"><a href="https://id.wikipedia.org/wiki/Format_FASTQ" title="Format FASTQ – Indonesian" lang="id" hreflang="id" data-title="Format FASTQ" data-language-autonym="Bahasa Indonesia" data-language-local-name="Indonesian" class="interlanguage-link-target"><span>Bahasa Indonesia</span></a></li><li class="interlanguage-link interwiki-he mw-list-item"><a href="https://he.wikipedia.org/wiki/%D7%A4%D7%95%D7%A8%D7%9E%D7%98_FASTQ" title="פורמט FASTQ – Hebrew" lang="he" hreflang="he" data-title="פורמט FASTQ" data-language-autonym="עברית" data-language-local-name="Hebrew" class="interlanguage-link-target"><span>עברית</span></a></li><li class="interlanguage-link interwiki-ja mw-list-item"><a href="https://ja.wikipedia.org/wiki/Fastq" title="Fastq – Japanese" lang="ja" hreflang="ja" data-title="Fastq" data-language-autonym="日本語" data-language-local-name="Japanese" class="interlanguage-link-target"><span>日本語</span></a></li><li class="interlanguage-link interwiki-pt mw-list-item"><a href="https://pt.wikipedia.org/wiki/Formato_FASTQ" title="Formato FASTQ – Portuguese" lang="pt" hreflang="pt" data-title="Formato FASTQ" 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.navbar{font-size:100%}@media screen{html.skin-theme-clientpref-night .mw-parser-output .infobox-full-data:not(.notheme)>div:not(.notheme)[style]{background:#1f1f23!important;color:#f8f9fa}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .infobox-full-data:not(.notheme) div:not(.notheme){background:#1f1f23!important;color:#f8f9fa}}@media(min-width:640px){body.skin--responsive .mw-parser-output .infobox-table{display:table!important}body.skin--responsive .mw-parser-output .infobox-table>caption{display:table-caption!important}body.skin--responsive .mw-parser-output .infobox-table>tbody{display:table-row-group}body.skin--responsive .mw-parser-output .infobox-table tr{display:table-row!important}body.skin--responsive .mw-parser-output .infobox-table th,body.skin--responsive .mw-parser-output .infobox-table td{padding-left:inherit;padding-right:inherit}}</style><table class="infobox"><caption class="infobox-title" style="padding-bottom: 0.15em;">FASTQ format</caption><tbody><tr><th scope="row" class="infobox-label" style="line-height: 1.2; padding-right: 0.65em;"><a href="/wiki/Media_type" title="Media type">Internet media type</a></th><td class="infobox-data" style="line-height: 1.35;">text/plain</td></tr><tr><th scope="row" class="infobox-label" style="line-height: 1.2; padding-right: 0.65em;">Developed by</th><td class="infobox-data" style="line-height: 1.35;"><a href="/wiki/Wellcome_Trust_Sanger_Institute" class="mw-redirect" title="Wellcome Trust Sanger Institute">Wellcome Trust Sanger Institute</a></td></tr><tr><th scope="row" class="infobox-label" style="line-height: 1.2; padding-right: 0.65em;">Initial release</th><td class="infobox-data" style="line-height: 1.35;">~2000</td></tr><tr><th scope="row" class="infobox-label" style="line-height: 1.2; padding-right: 0.65em;">Type of format</th><td class="infobox-data" style="line-height: 1.35;"><a href="/wiki/Bioinformatics" title="Bioinformatics">Bioinformatics</a></td></tr><tr><th scope="row" class="infobox-label" style="line-height: 1.2; padding-right: 0.65em;">Extended from</th><td class="infobox-data" style="line-height: 1.35;"><a href="/wiki/ASCII" title="ASCII">ASCII</a> and <a href="/wiki/FASTA_format" title="FASTA format">FASTA format</a></td></tr><tr><th scope="row" class="infobox-label" style="line-height: 1.2; padding-right: 0.65em;">Website</th><td class="infobox-data" style="line-height: 1.35;"><span class="url"><a rel="nofollow" class="external text" href="http://maq.sourceforge.net/fastq.shtml">maq<wbr />.sourceforge<wbr />.net<wbr />/fastq<wbr />.shtml</a></span></td></tr></tbody></table><p><b>FASTQ format</b> is a text-based <a href="/wiki/File_format" title="File format">format</a> for storing both a biological sequence (usually <a href="/wiki/Nucleotide_sequence" class="mw-redirect" title="Nucleotide sequence">nucleotide sequence</a>) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single <a href="/wiki/ASCII" title="ASCII">ASCII</a> character for brevity. </p><p>It was originally developed at the <a href="/wiki/Wellcome_Trust_Sanger_Institute" class="mw-redirect" title="Wellcome Trust Sanger Institute">Wellcome Trust Sanger Institute</a> to bundle a <a href="/wiki/FASTA_format" title="FASTA format">FASTA formatted</a> sequence and its quality data, but has become the <i><a href="/wiki/De_facto" title="De facto">de facto</a></i> standard for storing the output of high-throughput sequencing instruments such as the <a href="/wiki/Illumina_(company)" class="mw-redirect" title="Illumina (company)">Illumina</a> Genome Analyzer.<sup id="cite_ref-Cock2009_1-0" class="reference"><a href="#cite_note-Cock2009-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Format">Format</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=1" title="Edit section: Format"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>A FASTQ file has four line-separated fields per sequence: </p> <ul><li>Field 1 begins with a '@' character and is followed by a sequence identifier and an <i>optional</i> description (like a <a href="/wiki/FASTA_format" title="FASTA format">FASTA</a> title line).</li> <li>Field 2 is the raw sequence letters.</li> <li>Field 3 begins with a '+' character and is <i>optionally</i> followed by the same sequence identifier (and any description) again.</li> <li>Field 4 encodes the quality values for the sequence in Field 2, and must contain the same number of symbols as letters in the sequence.</li></ul> <p>A FASTQ file containing a single sequence might look like this: </p> <pre>@SEQ_ID GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT + !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 </pre> <p>The byte representing quality runs from 0x21 (lowest quality; '!' in ASCII) to 0x7e (highest quality; '~' in ASCII). Here are the quality value characters in left-to-right increasing order of quality (<a href="/wiki/ASCII" title="ASCII">ASCII</a>): </p> <pre>!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ </pre> <p>The original Sanger FASTQ files split long sequences and quality strings over multiple lines, as is typically done for <a href="/wiki/FASTA_format" title="FASTA format">FASTA</a> files. Accounting for this makes parsing more complicated due to the choice of "@" and "+" as markers (as these characters can also occur in the quality string). Multi-line FASTQ files (and consequently multi-line FASTQ parsers) are less common now that the majority of sequencing carried out is short-read <a href="/wiki/Illumina_dye_sequencing" title="Illumina dye sequencing">Illumina sequencing</a>, with typical sequence lengths of around 100bp. </p> <div class="mw-heading mw-heading3"><h3 id="Illumina_sequence_identifiers">Illumina sequence identifiers</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=2" title="Edit section: Illumina sequence identifiers"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Sequences from the <a href="/wiki/Solexa" class="mw-redirect" title="Solexa">Illumina</a> software use a systematic identifier: </p> <div class="mw-highlight mw-highlight-lang-unixconfig mw-content-ltr" dir="ltr"><pre><span></span><span class="s">@HWUSI-EAS100R</span><span class="p">:</span><span class="m">6</span><span class="p">:</span><span class="m">73</span><span class="p">:</span><span class="m">941</span><span class="p">:</span><span class="m">1973</span><span class="s">#0/1</span> </pre></div> <table class="wikitable"> <tbody><tr> <th>HWUSI-EAS100R </th> <td>the unique instrument name </td></tr> <tr> <th>6 </th> <td>flowcell lane </td></tr> <tr> <th>73 </th> <td>tile number within the flowcell lane </td></tr> <tr> <th>941 </th> <td>'x'-coordinate of the cluster within the tile </td></tr> <tr> <th>1973 </th> <td>'y'-coordinate of the cluster within the tile </td></tr> <tr> <th>#0 </th> <td>index number for a multiplexed sample (0 for no indexing) </td></tr> <tr> <th>/1 </th> <td>the member of a pair, /1 or /2 <i>(paired-end or mate-pair reads only)</i> </td></tr></tbody></table> <p>Versions of the Illumina pipeline since 1.4 appear to use <b>#NNNNNN</b> instead of <b>#0</b> for the multiplex ID, where <b>NNNNNN</b> is the sequence of the multiplex tag. </p><p>With Casava 1.8 the format of the '@' line has changed: </p> <div class="mw-highlight mw-highlight-lang-unixconfig mw-content-ltr" dir="ltr"><pre><span></span><span class="s">@EAS139</span><span class="p">:</span><span class="m">136</span><span class="p">:</span>FC706VJ<span class="p">:</span><span class="m">2</span><span class="p">:</span><span class="m">2104</span><span class="p">:</span><span class="m">15343</span><span class="p">:</span><span class="m">197393</span> 1<span class="p">:</span><span class="s">Y</span><span class="p">:</span><span class="m">18</span><span class="p">:</span>ATCACG </pre></div> <table class="wikitable"> <tbody><tr> <th>EAS139 </th> <td>the unique instrument name </td></tr> <tr> <th>136 </th> <td>the run id </td></tr> <tr> <th>FC706VJ </th> <td>the flowcell id </td></tr> <tr> <th>2 </th> <td>flowcell lane </td></tr> <tr> <th>2104 </th> <td>tile number within the flowcell lane </td></tr> <tr> <th>15343 </th> <td>'x'-coordinate of the cluster within the tile </td></tr> <tr> <th>197393 </th> <td>'y'-coordinate of the cluster within the tile </td></tr> <tr> <th>1 </th> <td>the member of a pair, 1 or 2 <i>(paired-end or mate-pair reads only)</i> </td></tr> <tr> <th>Y </th> <td>Y if the read is filtered (did not pass), N otherwise </td></tr> <tr> <th>18 </th> <td>0 when none of the control bits are on, otherwise it is an even number </td></tr> <tr> <th>ATCACG </th> <td>index sequence </td></tr></tbody></table> <p>Note that more recent versions of Illumina software output a sample number (defined by the order of the samples in the sample sheet) in place of an index sequence when an index sequence is not explicitly specified for a sample in the sample sheet. For example, the following header might appear in a FASTQ file belonging to the first sample of a batch of samples: </p> <div class="mw-highlight mw-highlight-lang-unixconfig mw-content-ltr" dir="ltr"><pre><span></span><span class="s">@EAS139</span><span class="p">:</span><span class="m">136</span><span class="p">:</span>FC706VJ<span class="p">:</span><span class="m">2</span><span class="p">:</span><span class="m">2104</span><span class="p">:</span><span class="m">15343</span><span class="p">:</span><span class="m">197393</span> 1<span class="p">:</span><span class="s">N</span><span class="p">:</span><span class="m">18</span><span class="p">:</span><span class="m">1</span> </pre></div> <div class="mw-heading mw-heading3"><h3 id="NCBI_Sequence_Read_Archive">NCBI Sequence Read Archive</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=3" title="Edit section: NCBI Sequence Read Archive"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>FASTQ files from the <a href="/wiki/International_Nucleotide_Sequence_Database_Collaboration" title="International Nucleotide Sequence Database Collaboration">INSDC</a> <a href="/wiki/Sequence_Read_Archive" title="Sequence Read Archive">Sequence Read Archive</a> often include a description, e.g. </p> <div class="mw-highlight mw-highlight-lang-unixconfig mw-content-ltr" dir="ltr"><pre><span></span><span class="s">@SRR001666.1 071112_SLXA-EAS1_s_7</span><span class="p">:</span><span class="m">5</span><span class="p">:</span><span class="m">1</span><span class="p">:</span><span class="m">817</span><span class="p">:</span><span class="m">345</span> length<span class="s">=36</span> GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC <span class="s">+SRR001666.1 071112_SLXA-EAS1_s_7</span><span class="p">:</span><span class="m">5</span><span class="p">:</span><span class="m">1</span><span class="p">:</span><span class="m">817</span><span class="p">:</span><span class="m">345</span> length<span class="s">=36</span> IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC </pre></div> <p>In this example there is an NCBI-assigned identifier, and the description holds the original identifier from <a href="/wiki/Solexa" class="mw-redirect" title="Solexa">Solexa/Illumina</a> (as described above) plus the read length. Sequencing was performed in paired-end mode (~500bp insert size), see <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/sra/SRR001666">SRR001666</a>. The default output format of fastq-dump produces entire spots, containing any technical reads and typically single or paired-end biological reads. </p> <div class="mw-highlight mw-highlight-lang-console mw-content-ltr" dir="ltr"><pre><span></span><span class="gp">$ </span>fastq-dump.2.9.0<span class="w"> </span>-Z<span class="w"> </span>-X<span class="w"> </span><span class="m">2</span><span class="w"> </span>SRR001666 <span class="go">Read 2 spots for SRR001666</span> <span class="go">Written 2 spots for SRR001666</span> <span class="go">@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72</span> <span class="go">GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA</span> <span class="go">+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/</span> <span class="go">@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72</span> <span class="go">GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT</span> <span class="go">+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I</span> </pre></div> <p>Modern usage of FASTQ almost always involves splitting the spot into its biological reads, as described in submitter-provided metadata: </p> <div class="mw-highlight mw-highlight-lang-console mw-content-ltr" dir="ltr"><pre><span></span><span class="gp">$ </span>fastq-dump<span class="w"> </span>-X<span class="w"> </span><span class="m">2</span><span class="w"> </span>SRR001666<span class="w"> </span>--split-3 <span class="go">Read 2 spots for SRR001666</span> <span class="go">Written 2 spots for SRR001666</span> <span class="gp">$ </span>head<span class="w"> </span>SRR001666_1.fastq<span class="w"> </span>SRR001666_2.fastq <span class="go">==> SRR001666_1.fastq <==</span> <span class="go">@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36</span> <span class="go">GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC</span> <span class="go">+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC</span> <span class="go">@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=36</span> <span class="go">GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA</span> <span class="go">+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=36</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBI</span> <span class="go">==> SRR001666_2.fastq <==</span> <span class="go">@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36</span> <span class="go">AAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA</span> <span class="go">+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36</span> <span class="go">IIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/</span> <span class="go">@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=36</span> <span class="go">AGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT</span> <span class="go">+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=36</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I</span> </pre></div> <p>When present in the archive, fastq-dump can attempt to restore read names to original format. NCBI does not store original read names by default: </p> <div class="mw-highlight mw-highlight-lang-console mw-content-ltr" dir="ltr"><pre><span></span><span class="gp">$ </span>fastq-dump<span class="w"> </span>-X<span class="w"> </span><span class="m">2</span><span class="w"> </span>SRR001666<span class="w"> </span>--split-3<span class="w"> </span>--origfmt <span class="go">Read 2 spots for SRR001666</span> <span class="go">Written 2 spots for SRR001666</span> <span class="gp">$ </span>head<span class="w"> </span>SRR001666_1.fastq<span class="w"> </span>SRR001666_2.fastq <span class="go">==> SRR001666_1.fastq <==</span> <span class="go">@071112_SLXA-EAS1_s_7:5:1:817:345</span> <span class="go">GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC</span> <span class="go">+071112_SLXA-EAS1_s_7:5:1:817:345</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC</span> <span class="go">@071112_SLXA-EAS1_s_7:5:1:801:338</span> <span class="go">GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA</span> <span class="go">+071112_SLXA-EAS1_s_7:5:1:801:338</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBI</span> <span class="go">==> SRR001666_2.fastq <==</span> <span class="go">@071112_SLXA-EAS1_s_7:5:1:817:345</span> <span class="go">AAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA</span> <span class="go">+071112_SLXA-EAS1_s_7:5:1:817:345</span> <span class="go">IIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/</span> <span class="go">@071112_SLXA-EAS1_s_7:5:1:801:338</span> <span class="go">AGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT</span> <span class="go">+071112_SLXA-EAS1_s_7:5:1:801:338</span> <span class="go">IIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I</span> </pre></div> <p>In the example above, the original read names were used rather than the accessioned read name. NCBI accessions runs and the reads they contain. Original read names, assigned by sequencers, are able to function as locally unique identifiers of a read, and convey exactly as much information as a serial number. The ids above were algorithmically assigned based upon run information and geometric coordinates. Early SRA loaders parsed these ids and stored their decomposed components internally. NCBI stopped recording read names because they are frequently modified from the vendors' original format in order to associate some additional information meaningful to a particular processing pipeline, and this caused name format violations that resulted in a high number of rejected submissions. Without a clear schema for read names, their function remains that of a unique read id, conveying the same amount of information as a read serial number. See various <a rel="nofollow" class="external text" href="https://github.com/ncbi/sra-tools/issues?q=is%3Aissue+original+read+names">SRA Toolkit issues</a> for details and discussions. </p><p>Also note that <a rel="nofollow" class="external text" href="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump">fastq-dump</a> converts this FASTQ data from the original Solexa/Illumina encoding to the Sanger standard (see encodings below). This is because <a rel="nofollow" class="external text" href="https://github.com/ncbi/sra-tools/issues/130#issuecomment-409995254">the SRA serves as a repository for NGS information, rather than format</a>. The various *-dump tools are capable of producing data in several formats from the same source. The requirements for doing so have been dictated by users over several years, with the majority of early demand coming from the <a href="/wiki/1000_Genomes_Project" title="1000 Genomes Project">1000 Genomes Project</a>. </p> <div class="mw-heading mw-heading2"><h2 id="Variations">Variations</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=4" title="Edit section: Variations"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Quality">Quality</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=5" title="Edit section: Quality"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>A quality value <i>Q</i> is an integer mapping of <i>p</i> (i.e., the probability that the corresponding base call is incorrect). Two different equations have been in use. The first is the standard Sanger variant to assess reliability of a base call, otherwise known as <a href="/wiki/Phred_quality_score" title="Phred quality score">Phred quality score</a>: </p> <dl><dd><span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle Q_{\text{sanger}}=-10\,\log _{10}p}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <msub> <mi>Q</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>sanger</mtext> </mrow> </msub> <mo>=</mo> <mo>−</mo> <mn>10</mn> <mspace width="thinmathspace"></mspace> <msub> <mi>log</mi> <mrow class="MJX-TeXAtom-ORD"> <mn>10</mn> </mrow> </msub> <mo>⁡</mo> <mi>p</mi> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle Q_{\text{sanger}}=-10\,\log _{10}p}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/d35e9473c8fb52974f7f37c6bd66852e2e276da3" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -1.005ex; width:21.061ex; height:2.843ex;" alt="{\displaystyle Q_{\text{sanger}}=-10\,\log _{10}p}" /></span></dd></dl> <p>The Solexa pipeline (i.e., the software delivered with the Illumina Genome Analyzer) earlier used a different mapping, encoding the <a href="/wiki/Odds" title="Odds">odds</a> <i>p</i>/(1-<i>p</i>) instead of the probability <i>p</i>: </p> <dl><dd><span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle Q_{\text{solexa-prior to v.1.3}}=-10\,\log _{10}{\frac {p}{1-p}}}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <msub> <mi>Q</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>solexa-prior to v.1.3</mtext> </mrow> </msub> <mo>=</mo> <mo>−</mo> <mn>10</mn> <mspace width="thinmathspace"></mspace> <msub> <mi>log</mi> <mrow class="MJX-TeXAtom-ORD"> <mn>10</mn> </mrow> </msub> <mo>⁡</mo> <mrow class="MJX-TeXAtom-ORD"> <mfrac> <mi>p</mi> <mrow> <mn>1</mn> <mo>−</mo> <mi>p</mi> </mrow> </mfrac> </mrow> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle Q_{\text{solexa-prior to v.1.3}}=-10\,\log _{10}{\frac {p}{1-p}}}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/ca73445cc28b13f2bde5997fe4499011de514bcc" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -2.338ex; width:35.747ex; height:5.343ex;" alt="{\displaystyle Q_{\text{solexa-prior to v.1.3}}=-10\,\log _{10}{\frac {p}{1-p}}}" /></span></dd></dl> <p>Although both mappings are asymptotically identical at higher quality values, they differ at lower quality levels (i.e., approximately <i>p</i> > 0.05, or equivalently, <i>Q</i> < 13). </p> <figure class="mw-halign-left" typeof="mw:File/Thumb"><a href="/wiki/File:Probability_metrics.svg" class="mw-file-description"><img alt="Relationship between Q and p" src="//upload.wikimedia.org/wikipedia/commons/thumb/6/6b/Probability_metrics.svg/600px-Probability_metrics.svg.png" decoding="async" width="600" height="350" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/6/6b/Probability_metrics.svg/900px-Probability_metrics.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/6/6b/Probability_metrics.svg/1200px-Probability_metrics.svg.png 2x" data-file-width="774" data-file-height="451" /></a><figcaption>Relationship between <i>Q</i> and <i>p</i> using the Sanger (red) and Solexa (black) equations (described above). The vertical dotted line indicates <i>p</i> = 0.05, or equivalently, <i>Q</i> ≈ 13.</figcaption></figure> <div style="clear:both;" class=""></div> <p>At times there has been disagreement about which mapping Illumina actually uses. The user guide (Appendix B, page 122) for version 1.4 of the Illumina pipeline states that: "The scores are defined as <span class="nowrap">⁠<span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle Q=10\cdot \log _{10}{\tfrac {p}{1-p}}}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <mi>Q</mi> <mo>=</mo> <mn>10</mn> <mo>⋅</mo> <msub> <mi>log</mi> <mrow class="MJX-TeXAtom-ORD"> <mn>10</mn> </mrow> </msub> <mo>⁡</mo> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="false" scriptlevel="0"> <mfrac> <mi>p</mi> <mrow> <mn>1</mn> <mo>−</mo> <mi>p</mi> </mrow> </mfrac> </mstyle> </mrow> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle Q=10\cdot \log _{10}{\tfrac {p}{1-p}}}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/20fd051f508556b6e1d72adfd03903c8aa7a566d" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -1.505ex; width:17.939ex; height:3.843ex;" alt="{\displaystyle Q=10\cdot \log _{10}{\tfrac {p}{1-p}}}" /></span>⁠</span>  [<i><a href="/wiki/Sic" title="Sic">sic</a></i>], where <span class="texhtml mvar" style="font-style:italic;">p</span> is the probability of a base call corresponding to the base in question".<sup id="cite_ref-Illumina_User_Guide_1.4_2-0" class="reference"><a href="#cite_note-Illumina_User_Guide_1.4-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> In retrospect, this entry in the manual appears to have been an error. The user guide (What's New, page 5) for version 1.5 of the Illumina pipeline lists this description instead: "Important Changes in Pipeline v1.3  [<i><a href="/wiki/Sic" title="Sic">sic</a></i>]. The quality scoring scheme has changed to the Phred [i.e., Sanger] scoring scheme, encoded as an ASCII character by adding 64 to the Phred value. A Phred score of a base is: <span class="mwe-math-element"><span class="mwe-math-mathml-inline mwe-math-mathml-a11y" style="display: none;"><math xmlns="http://www.w3.org/1998/Math/MathML" alttext="{\displaystyle Q_{\text{phred}}=-10\log _{10}e}"> <semantics> <mrow class="MJX-TeXAtom-ORD"> <mstyle displaystyle="true" scriptlevel="0"> <msub> <mi>Q</mi> <mrow class="MJX-TeXAtom-ORD"> <mtext>phred</mtext> </mrow> </msub> <mo>=</mo> <mo>−</mo> <mn>10</mn> <msub> <mi>log</mi> <mrow class="MJX-TeXAtom-ORD"> <mn>10</mn> </mrow> </msub> <mo>⁡</mo> <mi>e</mi> </mstyle> </mrow> <annotation encoding="application/x-tex">{\displaystyle Q_{\text{phred}}=-10\log _{10}e}</annotation> </semantics> </math></span><img src="https://wikimedia.org/api/rest_v1/media/math/render/svg/52711c8f2bbf23f584d917e086aaef72fde6d01c" class="mwe-math-fallback-image-inline mw-invert skin-invert" aria-hidden="true" style="vertical-align: -1.005ex; width:20.124ex; height:2.843ex;" alt="{\displaystyle Q_{\text{phred}}=-10\log _{10}e}" /></span>, where <i>e</i> is the estimated probability of a base being wrong.<sup id="cite_ref-Illumina_User_Guide_1.5_3-0" class="reference"><a href="#cite_note-Illumina_User_Guide_1.5-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Encoding">Encoding</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=6" title="Edit section: Encoding"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li>Sanger format can encode a <a href="/wiki/Phred_quality_score" title="Phred quality score">Phred quality score</a> from 0 to 93 using ASCII 33 to 126 (although in raw read data the Phred quality score rarely exceeds 60, higher scores are possible in assemblies or read maps). Also used in SAM format.<sup id="cite_ref-Sequence/Alignment_Map_format_4-0" class="reference"><a href="#cite_note-Sequence/Alignment_Map_format-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> Coming to the end of February 2011, Illumina's newest version (1.8) of their pipeline CASAVA will directly produce fastq in Sanger format, according to the announcement on seqanswers.com forum.<sup id="cite_ref-Upcoming_changes_in_CASAVA_topic_5-0" class="reference"><a href="#cite_note-Upcoming_changes_in_CASAVA_topic-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup></li> <li>Element Biosciences AVITI reads are encoded following the Sanger convention: Phred quality scores from 0 to 93 are encoded using ASCII 33 to 126. Raw reads typically exhibit base quality scores in the range of [0, 55]. <sup id="cite_ref-Elembio_AVITI_FASTQ_format_specification_6-0" class="reference"><a href="#cite_note-Elembio_AVITI_FASTQ_format_specification-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup></li> <li>PacBio HiFi reads, which are typically stored in SAM/BAM format, use the Sanger convention: Phred quality scores from 0 to 93 are encoded using ASCII 33 to 126. Raw PacBio subreads use the same convention but typically assign a placeholder base quality (Q0) to all bases in the read.<sup id="cite_ref-PacBio_BAM_format_specification_7-0" class="reference"><a href="#cite_note-PacBio_BAM_format_specification-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup></li> <li>Oxford Nanopore Duplex reads, called using the dorado basecaller are typically stored in SAM/BAM format. After changing to a 16-bit internal quality representation, the reported base quality limit is q50 (S).<sup id="cite_ref-Duplex-dorado_8-0" class="reference"><a href="#cite_note-Duplex-dorado-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup></li> <li>Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using <a href="/wiki/ASCII" title="ASCII">ASCII</a> 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)</li> <li>Starting with Illumina 1.3 and before Illumina 1.8, the format encoded a <a href="/wiki/Phred_quality_score" title="Phred quality score">Phred quality score</a> from 0 to 62 using <a href="/wiki/ASCII" title="ASCII">ASCII</a> 64 to 126 (although in raw read data Phred scores from 0 to 40 only are expected).</li> <li>Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a <i>Read Segment Quality Control Indicator</i>.<sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> The Illumina manual<sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> (page 30) states the following: <i>If a read ends with a segment of mostly low quality (Q15 or below), then all of the quality values in the segment are replaced with a value of 2 (encoded as the letter B in Illumina's text-based encoding of quality scores)... This Q2 indicator does not predict a specific error rate, but rather indicates that a specific final portion of the read should not be used in further analyses.</i> Also, the quality score encoded as "B" letter may occur internally within reads at least as late as pipeline version 1.6, as shown in the following example:</li></ul> <pre>@HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1 TTAATTGGTAAATAAATCTCCTAATAGCTTAGATNTTACCTTNNNNNNNNNNTAGTTTCTTGAGATTTGTTGGGGGAGACATTTTTGTGATTGCCTTGAT +HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1 efcfffffcfeefffcffffffddf`feed]`]_Ba_^__[YBBBBBBBBBBRTT\]][]dddd`ddd^dddadd^BBBBBBBBBBBBBBBBBBBBBBBB </pre> <p>An alternative interpretation of this ASCII encoding has been proposed.<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> Also, in Illumina runs using PhiX controls, the character 'B' was observed to represent an "unknown quality score". The error rate of 'B' reads was roughly 3 phred scores lower the mean observed score of a given run. </p> <ul><li>Starting in Illumina 1.8, the quality scores have basically returned to the use of the Sanger format (Phred+33).</li></ul> <p>For raw reads, the range of scores will depend on the technology and the base caller used, but will typically be up to 41 for recent Illumina chemistry. Since the maximum observed quality score was previously only 40, various scripts and tools break when they encounter data with quality values larger than 40. For processed reads, scores may be even higher. For example, quality values of 45 are observed in reads from Illumina's Long Read Sequencing Service (previously Moleculo). </p> <pre> <span style="color: purple">SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS</span>..................................................... ..........................<span style="color: green">XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</span>...................... ...............................<span style="color: #CC5500">IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII</span>...................... .................................<span style="color: #FFA500"><b>J</b>JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ</span>..................... <span style="color: #FF7518">LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL</span>.................................................... <span style="color: steelblue">NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...........................................</span> <span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EEEEEE</span><span style="color: blue">EE</span> <span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPPPP</span><span style="color: red">PPPP</span>  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ | | | | | | | 33 59 64 73 88 104 126 <span style="color: purple"> 0........................26...31.......40 </span> <span style="color: green"> -5....0........9.............................40 </span> <span style="color: #CC5500"> 0........9.............................40 </span> <span style="color: #FFA500"> 3.....9..............................41 </span> <span style="color: #FF7518"> 0.2......................26...31........41 </span> <span style="color: steelblue"> 0..................20........30........40........50</span> <span style="color: blue"> 0..................20........30........40........50...55</span> <span style="color: red"> 0..................20........30........40........50..........................................93</span> </pre> <pre> <span style="color: purple">S - Sanger Phred+33, raw reads typically (0, 40)</span> <span style="color: green">X - Solexa Solexa+64, raw reads typically (-5, 40)</span> <span style="color: #CC5500">I - Illumina 1.3+ Phred+64, raw reads typically (0, 40)</span> <span style="color: #FFA500">J - Illumina 1.5+ Phred+64, raw reads typically (3, 41) with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) (Note: See discussion above).</span> <span style="color: #FF7518">L - Illumina 1.8+ Phred+33, raw reads typically (0, 41)</span> <span style="color: steelblue">N - Nanopore Phred+33, Duplex reads typically (0, 50)</span> <span style="color: blue">E - ElemBio AVITI Phred+33, raw reads typically (0, 55)</span> <span style="color: red">P - PacBio Phred+33, HiFi reads typically (0, 93)</span> </pre> <div class="mw-heading mw-heading3"><h3 id="Color_space">Color space</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=7" title="Edit section: Color space"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>For SOLiD data, the format is modified to a color space FASTQ sequence (CSFASTQ), where bases in the sequence are combined with the numbers 0, 1, 2, and 3, indicating how bases are modified relative to the previous base in the sequence (0: no change; 1: transition; 2: non-complementary transversion; 3: complementary transversion).<sup id="cite_ref-Cock2009_1-1" class="reference"><a href="#cite_note-Cock2009-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> This format matched the different sequencing chemistry used by SOLiD sequencers. Initial representations only used nucleotide bases at the start of the sequence, but later versions included bases embedded at periodic intervals to improve basecalling and mapping accuracy. </p><p>The quality values for CSFASTQ are identical to those of the Sanger format. Alignment tools differ in their preferred version of the quality values: some include a quality score (set to 0, i.e. '!') for the leading nucleotide, others do not. The sequence read archive includes this quality score. </p> <div class="mw-heading mw-heading3"><h3 id="FAST5_and_HDF5_evolutions">FAST5 and HDF5 evolutions</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=8" title="Edit section: FAST5 and HDF5 evolutions"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The FAST4 format was invented as a derivative of the FASTQ format where each of the 4 bases (A,C,G,T) had separate probabilities stored. It was part of the <a href="https://sourceforge.net/p/swiftng" class="extiw" title="sourceforge:p/swiftng">Swift</a> basecaller, an open source package for primary data analysis on next-gen sequence data "from images to basecalls". </p><p>The FAST5 format was invented as an extension of the FAST4 format. The FAST5 files are <a href="/wiki/Hierarchical_Data_Format" title="Hierarchical Data Format">Hierarchical Data Format 5</a> (HDF5) files with a specific schema defined by <a href="/wiki/Oxford_Nanopore_Technologies" title="Oxford Nanopore Technologies">Oxford Nanopore Technologies</a> (ONT).<sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Simulation">Simulation</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=9" title="Edit section: Simulation"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>FASTQ read simulation has been approached by several tools.<sup id="cite_ref-13" class="reference"><a href="#cite_note-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-14" class="reference"><a href="#cite_note-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> A comparison of those tools can be seen here.<sup id="cite_ref-15" class="reference"><a href="#cite_note-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Compression">Compression</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=10" title="Edit section: Compression"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading4"><h4 id="General_compressors">General compressors</h4><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=11" title="Edit section: General compressors"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>General-purpose tools such as Gzip and bzip2 regard FASTQ as a plain text file and result in suboptimal compression ratios. NCBI's <a href="/wiki/Sequence_Read_Archive" title="Sequence Read Archive">Sequence Read Archive</a> encodes metadata using the LZ-77 scheme. General FASTQ compressors typically compress distinct fields (read names, sequences, comments, and quality scores) in a FASTQ file separately; these include DSRC and DSRC2, FQC, LFQC, Fqzcomp, and Slimfastq. </p> <div class="mw-heading mw-heading4"><h4 id="Reads">Reads</h4><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=12" title="Edit section: Reads"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Having a reference genome around is convenient because then instead of storing the nucleotide sequences themselves, one can just align the reads to the reference genome and store the positions (pointers) and mismatches; the pointers can then be sorted according to their order in the reference sequence and encoded, e.g., with run-length encoding. When the <a href="/wiki/Coverage_(genetics)" title="Coverage (genetics)">coverage</a> or the repeat content of the sequenced genome is high, this leads to a high compression ratio. Unlike the <a href="/wiki/SAM_(file_format)" title="SAM (file format)">SAM</a>/BAM formats, FASTQ files do not specify a reference genome. <b>Alignment-based FASTQ compressors</b> supports the use of either user-provided or <i>de novo</i> assembled reference: LW-FQZip uses a provided reference genome and Quip, Leon, k-Path and KIC perform <i><b>de novo</b></i> assembly using a <a href="/wiki/De_Bruijn_graph" title="De Bruijn graph">de Bruijn graph</a>-based approach. </p><p>Explicit read mapping and <i>de novo</i> assembly are typically slow. <b>Reordering-based FASTQ compressors</b> first cluster reads that share long substrings and then independently compress reads in each cluster after reordering them or assembling them into longer <a href="/wiki/Contig" title="Contig">contigs</a>, achieving perhaps the best trade-off between the running time and compression rate. SCALCE is the first such tool, followed by Orcom and Mince. BEETL uses a generalized <a href="/wiki/Burrows%E2%80%93Wheeler_transform" title="Burrows–Wheeler transform">Burrows–Wheeler transform</a> for reordering reads, and HARC achieves better performance with hash-based reordering. AssemblTrie instead assembles reads into reference trees with as few total number of symbols as possible in the reference.<sup id="cite_ref-pmid29422526_16-0" class="reference"><a href="#cite_note-pmid29422526-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Zhu_Numanagić_Sahinalp_2018_pp._779-783_17-0" class="reference"><a href="#cite_note-Zhu_Numanagić_Sahinalp_2018_pp._779-783-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> </p><p>Benchmarks for these tools are available in.<sup id="cite_ref-Numanagić_Bonfield_Hach_Voges_pp._1005–1008_18-0" class="reference"><a href="#cite_note-Numanagić_Bonfield_Hach_Voges_pp._1005–1008-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading4"><h4 id="Quality_values">Quality values</h4><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=13" title="Edit section: Quality values"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Quality values account for about half of the required disk space in the FASTQ format (before compression), and therefore the compression of the quality values can significantly reduce storage requirements and speed up analysis and transmission of sequencing data. Both lossless and lossy compression are recently being considered in the literature. For example, the algorithm QualComp<sup id="cite_ref-19" class="reference"><a href="#cite_note-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> performs lossy compression with a rate (number of bits per quality value) specified by the user. Based on rate-distortion theory results, it allocates the number of bits so as to minimize the MSE (mean squared error) between the original (uncompressed) and the reconstructed (after compression) quality values. Other algorithms for compression of quality values include SCALCE<sup id="cite_ref-20" class="reference"><a href="#cite_note-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> and Fastqz.<sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup> Both are lossless compression algorithms that provide an optional controlled lossy transformation approach. For example, SCALCE reduces the alphabet size based on the observation that “neighboring” quality values are similar in general. For a benchmark, see.<sup id="cite_ref-Morteza_22-0" class="reference"><a href="#cite_note-Morteza-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> </p><p>As of the HiSeq 2500 Illumina gives the option to output qualities that have been coarse grained into quality bins. The binned scores are computed directly from the empirical quality score table, which is itself tied to the hardware, software and chemistry that were used during the sequencing experiment.<sup id="cite_ref-23" class="reference"><a href="#cite_note-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="File_extension">File extension</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=14" title="Edit section: File extension"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>There is no standard <a href="/wiki/File_extension" class="mw-redirect" title="File extension">file extension</a> for a FASTQ file, but .fq and .fastq are commonly used. </p> <div class="mw-heading mw-heading2"><h2 id="Format_converters">Format converters</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=15" title="Edit section: Format converters"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a href="/wiki/Biopython" title="Biopython">Biopython</a> version 1.51 onwards (interconverts Sanger, Solexa and Illumina 1.3+)</li> <li><a href="/wiki/EMBOSS" title="EMBOSS">EMBOSS</a> version 6.1.0 patch 1 onwards (interconverts Sanger, Solexa and Illumina 1.3+)</li> <li><a href="/wiki/BioPerl" title="BioPerl">BioPerl</a> version 1.6.1 onwards (interconverts Sanger, Solexa and Illumina 1.3+)</li> <li><a href="/wiki/BioRuby" title="BioRuby">BioRuby</a> version 1.4.0 onwards (interconverts Sanger, Solexa and Illumina 1.3+)</li> <li><a href="/wiki/BioJava" title="BioJava">BioJava</a> version 1.7.1 onwards (interconverts Sanger, Solexa and Illumina 1.3+)</li></ul> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=16" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li>The <a href="/wiki/FASTA_format" title="FASTA format">FASTA</a> format, used to represent genome sequences.</li> <li>The <a href="/wiki/SAM_(file_format)" title="SAM (file format)">SAM</a> and <a href="/wiki/CRAM_(file_format)" title="CRAM (file format)">CRAM</a> formats, used to represent genome sequencer reads that have been aligned to genome sequences.</li> <li>The <a href="/w/index.php?title=GVF_format&action=edit&redlink=1" class="new" title="GVF format (page does not exist)">GVF</a> format (Genome Variation Format), an extension based on the <a href="/wiki/GFF3" class="mw-redirect" title="GFF3">GFF3</a> format.</li></ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=FASTQ_format&action=edit&section=17" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist reflist-columns references-column-width" style="column-width: 35em;"> <ol class="references"> <li id="cite_note-Cock2009-1"><span class="mw-cite-backlink">^ <a href="#cite_ref-Cock2009_1-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-Cock2009_1-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFCockFieldsGotoHeuer2009" class="citation journal cs1">Cock, P. J. A.; Fields, C. J.; Goto, N.; Heuer, M. L.; Rice, P. M. (2009). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217">"The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants"</a>. <i>Nucleic Acids Research</i>. <b>38</b> (6): <span class="nowrap">1767–</span>1771. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fnar%2Fgkp1137">10.1093/nar/gkp1137</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217">2847217</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/20015970">20015970</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Nucleic+Acids+Research&rft.atitle=The+Sanger+FASTQ+file+format+for+sequences+with+quality+scores%2C+and+the+Solexa%2FIllumina+FASTQ+variants&rft.volume=38&rft.issue=6&rft.pages=%3Cspan+class%3D%22nowrap%22%3E1767-%3C%2Fspan%3E1771&rft.date=2009&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2847217%23id-name%3DPMC&rft_id=info%3Apmid%2F20015970&rft_id=info%3Adoi%2F10.1093%2Fnar%2Fgkp1137&rft.aulast=Cock&rft.aufirst=P.+J.+A.&rft.au=Fields%2C+C.+J.&rft.au=Goto%2C+N.&rft.au=Heuer%2C+M.+L.&rft.au=Rice%2C+P.+M.&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC2847217&rfr_id=info%3Asid%2Fen.wikipedia.org%3AFASTQ+format" class="Z3988"></span></span> </li> <li id="cite_note-Illumina_User_Guide_1.4-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-Illumina_User_Guide_1.4_2-0">^</a></b></span> <span class="reference-text">Sequencing Analysis Software User Guide: For Pipeline Version 1.4 and CASAVA Version 1.0, dated April 2009 <a rel="nofollow" class="external text" href="http://genomecenter.ucdavis.edu/dna_technologies/documents/pipeline_1_4.pdf">PDF</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20100610232559/http://genomecenter.ucdavis.edu/dna_technologies/documents/pipeline_1_4.pdf">Archived</a> June 10, 2010, at the <a href="/wiki/Wayback_Machine" title="Wayback Machine">Wayback Machine</a></span> </li> <li id="cite_note-Illumina_User_Guide_1.5-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-Illumina_User_Guide_1.5_3-0">^</a></b></span> <span class="reference-text">Sequencing Analysis Software User Guide: For Pipeline Version 1.5 and CASAVA Version 1.0, dated August 2009 <a rel="nofollow" class="external text" href="http://illumina.ucr.edu/illumina_docs/Pipeline1.5/Pipeline1.5_CASAVA1.0_User_Guide_15006500_A.pdf">PDF</a><sup class="noprint Inline-Template"><span style="white-space: nowrap;">[<i><a href="/wiki/Wikipedia:Link_rot" title="Wikipedia:Link rot"><span title=" Dead link tagged July 2015">dead link</span></a></i><span style="visibility:hidden; color:transparent; padding-left:2px">‍</span>]</span></sup></span> </li> <li id="cite_note-Sequence/Alignment_Map_format-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-Sequence/Alignment_Map_format_4-0">^</a></b></span> <span class="reference-text">Sequence/Alignment Map format Version 1.0, dated August 2009 <a rel="nofollow" class="external text" href="http://samtools.sourceforge.net/SAM1.pdf">PDF</a></span> </li> <li id="cite_note-Upcoming_changes_in_CASAVA_topic-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-Upcoming_changes_in_CASAVA_topic_5-0">^</a></b></span> <span class="reference-text">Seqanswer's topic of skruglyak, dated January 2011 <a rel="nofollow" class="external text" href="http://seqanswers.com/forums/showthread.php?s=ba8c7dfba863815f637c0bf45882f14b&t=8895">website</a></span> </li> <li id="cite_note-Elembio_AVITI_FASTQ_format_specification-6"><span class="mw-cite-backlink"><b><a href="#cite_ref-Elembio_AVITI_FASTQ_format_specification_6-0">^</a></b></span> <span class="reference-text">Elembio AVITI FASTQ format specification <a rel="nofollow" class="external text" href="https://docs.elembio.io/docs/bases2fastq/outputs/#quality-scores">https://docs.elembio.io/docs/bases2fastq/outputs/#quality-scores</a></span> </li> <li id="cite_note-PacBio_BAM_format_specification-7"><span class="mw-cite-backlink"><b><a href="#cite_ref-PacBio_BAM_format_specification_7-0">^</a></b></span> <span class="reference-text">PacBio BAM format specification 10.0.0 <a rel="nofollow" class="external text" href="https://pacbiofileformats.readthedocs.io/en/10.0/BAM.html#qual">https://pacbiofileformats.readthedocs.io/en/10.0/BAM.html#qual</a></span> </li> <li id="cite_note-Duplex-dorado-8"><span class="mw-cite-backlink"><b><a href="#cite_ref-Duplex-dorado_8-0">^</a></b></span> <span class="reference-text">Dorado duplex basecalling guide [duplex-tools: usage with dorado <a rel="nofollow" class="external free" href="https://github.com/nanoporetech/duplex-tools#usage-with-dorado-recommended">https://github.com/nanoporetech/duplex-tools#usage-with-dorado-recommended</a>]</span> </li> <li id="cite_note-9"><span class="mw-cite-backlink"><b><a href="#cite_ref-9">^</a></b></span> <span class="reference-text">Illumina Quality Scores, Tobias Mann, Bioinformatics, San Diego, Illumina <a rel="nofollow" class="external free" href="http://seqanswers.com/forums/showthread.php?t=4721">http://seqanswers.com/forums/showthread.php?t=4721</a></span> </li> <li id="cite_note-10"><span class="mw-cite-backlink"><b><a href="#cite_ref-10">^</a></b></span> <span class="reference-text">Using Genome Analyzer Sequencing Control Software, Version 2.6, Catalog # SY-960-2601, Part # 15009921 Rev. 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href="http://maq.sourceforge.net/fastq.shtml">MAQ</a> webpage discussing FASTQ variants</li></ul> <div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist ul{margin:0;padding:0}.mw-parser-output .hlist dd,.mw-parser-output .hlist dt,.mw-parser-output .hlist li{margin:0;display:inline}.mw-parser-output .hlist.inline,.mw-parser-output .hlist.inline dl,.mw-parser-output .hlist.inline ol,.mw-parser-output .hlist.inline ul,.mw-parser-output .hlist dl dl,.mw-parser-output .hlist dl ol,.mw-parser-output .hlist dl ul,.mw-parser-output .hlist ol dl,.mw-parser-output .hlist ol ol,.mw-parser-output .hlist ol ul,.mw-parser-output .hlist ul dl,.mw-parser-output .hlist ul ol,.mw-parser-output .hlist ul ul{display:inline}.mw-parser-output .hlist .mw-empty-li{display:none}.mw-parser-output .hlist dt::after{content:": "}.mw-parser-output .hlist dd::after,.mw-parser-output .hlist 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class="navbox-group" style="width:1%">Databases</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Sequence databases: <a href="/wiki/GenBank" title="GenBank">GenBank</a>, <a href="/wiki/European_Nucleotide_Archive" title="European Nucleotide Archive">European Nucleotide Archive</a>, <a href="/wiki/DNA_Data_Bank_of_Japan" title="DNA Data Bank of Japan">DNA Data Bank of Japan</a> and <a href="/wiki/China_National_GeneBank" title="China National GeneBank">China National GeneBank</a></li> <li>Secondary databases: <a href="/wiki/UniProt" title="UniProt">UniProt</a>, database of protein sequences grouping together <a href="/wiki/UniProt#UniProtKB.2FSwiss-Prot" title="UniProt">Swiss-Prot</a>, <a href="/wiki/UniProt#UniProtKB.2FTrEMBL" title="UniProt">TrEMBL</a> and <a href="/wiki/Protein_Information_Resource" title="Protein Information Resource">Protein Information Resource</a></li> <li>Other databases: <a href="/wiki/BioNumbers" title="BioNumbers">BioNumbers</a>, <a href="/wiki/Protein_Data_Bank" title="Protein Data Bank">Protein Data Bank</a>, <a href="/wiki/Ensembl_genome_database_project" title="Ensembl genome database project">Ensembl</a>, <a href="/wiki/InterPro" title="InterPro">InterPro</a>, <a href="/wiki/KEGG" title="KEGG">KEGG</a>, and <a href="/wiki/Gene_ontology" class="mw-redirect" title="Gene ontology">Gene Ontology</a></li> <li>Specialised genomic databases: <a href="/wiki/Barcode_of_Life_Data_System" title="Barcode of Life Data System">BOLD</a>, <a href="/wiki/Saccharomyces_Genome_Database" title="Saccharomyces Genome Database">Saccharomyces Genome Database</a>, <a href="/wiki/FlyBase" title="FlyBase">FlyBase</a>, <a href="/wiki/VectorBase" title="VectorBase">VectorBase</a>, <a href="/wiki/WormBase" title="WormBase">WormBase</a>, <a href="/wiki/Rat_Genome_Database" title="Rat Genome Database">Rat Genome Database</a>, <a href="/wiki/PHI-base" title="PHI-base">PHI-base</a>, <a href="/wiki/The_Arabidopsis_Information_Resource" title="The Arabidopsis Information Resource">Arabidopsis Information Resource</a>, <a href="/wiki/GISAID" title="GISAID">GISAID</a> and <a href="/wiki/Zebrafish_Information_Network" title="Zebrafish Information Network">Zebrafish Information Network</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Software</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/BLAST_(biotechnology)" title="BLAST (biotechnology)">BLAST</a></li> <li><a href="/wiki/Bowtie_(sequence_analysis)" title="Bowtie (sequence analysis)">Bowtie</a></li> <li><a href="/wiki/Clustal" title="Clustal">Clustal</a></li> <li><a href="/wiki/EMBOSS" title="EMBOSS">EMBOSS</a></li> <li><a href="/wiki/HMMER" title="HMMER">HMMER</a></li> <li><a href="/wiki/MUSCLE_(alignment_software)" title="MUSCLE (alignment software)">MUSCLE</a></li> <li><a href="/wiki/Phylogenetic_Assignment_of_Named_Global_Outbreak_Lineages" title="Phylogenetic Assignment of Named Global Outbreak Lineages">PANGOLIN</a></li> <li><a href="/wiki/SAMtools" title="SAMtools">SAMtools</a></li> <li><a href="/wiki/Short_Oligonucleotide_Analysis_Package" title="Short Oligonucleotide Analysis Package">SOAP suite</a></li> <li><a href="/wiki/TopHat_(bioinformatics)" title="TopHat (bioinformatics)">TopHat</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Other</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Server: <a href="/wiki/ExPASy" class="mw-redirect" title="ExPASy">ExPASy</a></li> <li><a href="/wiki/Rosalind_(education_platform)" title="Rosalind (education platform)">Rosalind (education platform)</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Institutions</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Broad_Institute" title="Broad Institute">Broad Institute</a></li> <li><a href="/wiki/Computational_Biology_Department" class="mw-redirect" title="Computational Biology Department">Computational Biology Department</a> (CBD)</li> <li><a href="/wiki/COSBI" title="COSBI">Microsoft Research - University of Trento Centre for Computational and Systems Biology</a> (COSBI)</li> <li><a href="/wiki/Database_Center_for_Life_Science" title="Database Center for Life Science">Database Center for Life Science</a> (DBCLS)</li> <li><a href="/wiki/DNA_Data_Bank_of_Japan" title="DNA Data Bank of Japan">DNA Data Bank of Japan</a> (DDBJ)</li> <li><a href="/wiki/European_Bioinformatics_Institute" title="European Bioinformatics Institute">European Bioinformatics Institute</a> (EMBL-EBI)</li> <li><a href="/wiki/European_Molecular_Biology_Laboratory" title="European Molecular Biology Laboratory">European Molecular Biology Laboratory</a> (EMBL)</li> <li><a href="/wiki/Flatiron_Institute" title="Flatiron Institute">Flatiron Institute</a></li> <li><a href="/wiki/J._Craig_Venter_Institute" title="J. Craig Venter Institute">J. Craig Venter Institute</a> (JCVI)</li> <li><a href="/wiki/Max_Planck_Institute_of_Molecular_Cell_Biology_and_Genetics" title="Max Planck Institute of Molecular Cell Biology and Genetics">Max Planck Institute of Molecular Cell Biology and Genetics</a> (MPI-CBG)</li> <li><a href="/wiki/National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">US National Center for Biotechnology Information</a> (NCBI)</li> <li><a href="/wiki/National_Institute_of_Genetics" title="National Institute of Genetics">Japanese Institute of Genetics</a></li> <li><a href="/wiki/Netherlands_Bioinformatics_Centre" title="Netherlands Bioinformatics Centre">Netherlands Bioinformatics Centre</a> (NBIC)</li> <li><a href="/wiki/Philippine_Genome_Center" title="Philippine Genome Center">Philippine Genome Center</a> (PGC)</li> <li><a href="/wiki/Scripps_Research" title="Scripps Research">Scripps Research</a></li> <li><a href="/wiki/Swiss_Institute_of_Bioinformatics" title="Swiss Institute of Bioinformatics">Swiss Institute of Bioinformatics</a> (SIB)</li> <li><a href="/wiki/Wellcome_Sanger_Institute" title="Wellcome Sanger Institute">Wellcome Sanger Institute</a></li> <li><a href="/wiki/Whitehead_Institute" title="Whitehead Institute">Whitehead Institute</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Organizations</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/African_Society_for_Bioinformatics_and_Computational_Biology" title="African Society for Bioinformatics and Computational Biology">African Society for Bioinformatics and Computational Biology</a> (ASBCB)</li> <li><a href="/wiki/Australia_Bioinformatics_Resource" title="Australia Bioinformatics Resource">Australia Bioinformatics Resource</a> (EMBL-AR)</li> <li><a href="/wiki/EMBnet" title="EMBnet">European Molecular Biology network</a> (EMBnet)</li> <li><a href="/wiki/International_Nucleotide_Sequence_Database_Collaboration" title="International Nucleotide Sequence Database Collaboration">International Nucleotide Sequence Database Collaboration</a> (INSDC)</li> <li><a href="/wiki/International_Society_for_Biocuration" title="International Society for Biocuration">International Society for Biocuration</a> (ISB)</li> <li><a href="/wiki/International_Society_for_Computational_Biology" title="International Society for Computational Biology">International Society for Computational Biology</a> (ISCB) <ul><li><a href="/wiki/International_Society_for_Computational_Biology_Student_Council" title="International Society for Computational Biology Student Council">Student Council</a> (ISCB-SC)</li></ul></li> <li><a href="/wiki/Institute_of_Genomics_and_Integrative_Biology" title="Institute of Genomics and Integrative Biology">Institute of Genomics and Integrative Biology</a> (CSIR-IGIB)</li> <li><a href="/wiki/Japanese_Society_for_Bioinformatics" title="Japanese Society for Bioinformatics">Japanese Society for Bioinformatics</a> (JSBi)</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Meetings</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Basel_Computational_Biology_Conference" title="Basel Computational Biology Conference">Basel Computational Biology Conference‎</a> ([BC<sup>2</sup>])</li> <li><a href="/wiki/European_Conference_on_Computational_Biology" title="European Conference on Computational Biology">European Conference on Computational Biology</a> (ECCB)</li> <li><a href="/wiki/Intelligent_Systems_for_Molecular_Biology" title="Intelligent Systems for Molecular Biology">Intelligent Systems for Molecular Biology</a> (ISMB)</li> <li><a href="/wiki/International_Conference_on_Bioinformatics" title="International Conference on Bioinformatics">International Conference on Bioinformatics</a> (InCoB)</li> <li><a href="/wiki/International_Conference_on_Computational_Intelligence_Methods_for_Bioinformatics_and_Biostatistics" title="International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics">International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics</a> (CIBB)</li> <li><a href="/wiki/ISCB_Africa_ASBCB_Conference_on_Bioinformatics" title="ISCB Africa ASBCB Conference on Bioinformatics">ISCB Africa ASBCB Conference on Bioinformatics</a></li> <li><a href="/wiki/Pacific_Symposium_on_Biocomputing" title="Pacific Symposium on Biocomputing">Pacific Symposium on Biocomputing</a> (PSB)</li> <li><a href="/wiki/Research_in_Computational_Molecular_Biology" title="Research in Computational Molecular Biology">Research in Computational Molecular Biology</a> (RECOMB)</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">File formats</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/CRAM_(file_format)" title="CRAM (file format)">CRAM format</a></li> <li><a href="/wiki/FASTA_format" title="FASTA format">FASTA format</a></li> <li><a class="mw-selflink selflink">FASTQ format</a></li> <li><a href="/wiki/NeXML_format" title="NeXML format">NeXML format</a></li> <li><a href="/wiki/Nexus_file" title="Nexus file">Nexus format</a></li> <li><a href="/wiki/Pileup_format" title="Pileup format">Pileup format</a></li> <li><a href="/wiki/SAM_(file_format)" title="SAM (file format)">SAM format</a></li> <li><a href="/wiki/Stockholm_format" title="Stockholm format">Stockholm format</a></li> <li><a href="/wiki/Variant_Call_Format" title="Variant Call Format">VCF format</a></li> <li><a href="/wiki/General_feature_format" title="General feature format">GFF format</a></li> <li><a href="/wiki/Gene_transfer_format" title="Gene transfer format">GTF format</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Related topics</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Computational_biology" title="Computational biology">Computational biology</a></li> <li><a href="/wiki/List_of_biobanks" title="List of biobanks">List of biobanks</a></li> <li><a href="/wiki/List_of_biological_databases" title="List of biological databases">List of biological databases</a></li> <li><a href="/wiki/Molecular_phylogenetics" title="Molecular phylogenetics">Molecular phylogenetics</a></li> <li><a href="/wiki/Sequencing" title="Sequencing">Sequencing</a></li> <li><a href="/wiki/Sequence_database" title="Sequence database">Sequence database</a></li> <li><a href="/wiki/Sequence_alignment" title="Sequence alignment">Sequence alignment</a></li></ul> </div></td></tr><tr><td class="navbox-abovebelow hlist" colspan="2"><div> <ul><li><span 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