313 lines
12 KiB
Text
313 lines
12 KiB
Text
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<!DOCTYPE html>
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<title>Genome Assemblies - Genome Reference Consortium</title>
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<b>Warning:</b> this web site requires JavaScript to function. <a href="/guide/browsers#js_settings">more...</a>
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<img alt="GRC logo" src="/grc/static/grc/img/GRC_logo_reasonably_small.png" /><img src="/grc/static/grc/img/TitleBanner.png" alt="Genome Reference Consortium" /></a>
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<a id="skipnav" href="#main">Skip navigation and go to main content</a>
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<li><a href="/grc" title="GRC home" id="homeMenuItem">GRC Home</a></li>
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<li><a href="/grc/data" title="Data" id="dataMenuItem">Data</a>
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<li><a href="human" title="Go to human genome overview page">Human</a></li>
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<li><a href="mouse" title="Go to mouse genome overview page">Mouse</a></li>
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<li><a href="zebrafish" title="Go to zebrafish genome overview page">Zebrafish</a></li>
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<li><a href="rat" title="Go to rat genome overview page">Rat</a></li>
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<li><a href="chicken" title="Go to chicken genome overview page">Chicken</a></li>
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<li><a href="supplement" title="Go to Supplemental Data section">Paper Supplemental Data</a></li>
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</div><!--end menu-->
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<div id="main"><a name="main"></a>
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<div id="data">
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<div id="contents" style="overflow:hidden;">
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<h1>Genome Assemblies</h1>
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<div id="right_col">
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<div id="news" class="widget">
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<h3>
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<a href='http://genomeref.blogspot.com' target='_blank'>GRC News</a>
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</h3>
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<div id="news_items" class="content">
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<p class="issue_date">Feb 02, 2024</p>
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<h4><a href="http://genomeref.blogspot.com/2024/02/grcr8-new-rat-reference-assembly-is.html" title="View blog post" target="_blank">GRCr8: A new rat reference assembly is released!</a></h4>
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<br/>
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<p class="issue_date">May 09, 2022</p>
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<h4><a href="http://genomeref.blogspot.com/2022/05/grch38p14-is-now-released.html" title="View blog post" target="_blank">GRCh38.p14 is now released!</a></h4>
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<a href="http://genomeref.blogspot.com" class="more" title="View GRC blog">see all</a>
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</div>
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</div>
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</div>
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<p>The GRC has built tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences (clones and PCR products, not short sequence reads). The GRC currently supports production of assemblies for human, mouse or zebrafish. If your assembly data fits this model and you are interested in using these tools, please <a href="contact-us">contact us</a>. <a href="/mailman/listinfo/grc-announce">Subscribe</a> to the grc-announce email list to receive email notification for all GRC assembly updates.</p>
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<div class="spec_info" id="human">
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<div class="critters"><a href="human"><img src="/grc/static/grc/img/vitruvian_man.png" alt="Human" /></a></div>
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<div class="critter_info">
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<h2><a href="human">Human</a></h2>
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<p>The human genome assembly was produced as part of the <a href="http://www.genome.gov/10001772">Human Genome Project (HGP)</a>. The previous assembly (NCBI36) was the last one produced by the HGP and was described in 2004 (<a href="/pubmed/15496913" target="_blank">PMID: 15496913</a>); this was the starting point for the GRC. The assembly is based largely on assembling overlapping clone sequences.</p>
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<table class="brief_stats" summary="Brief stats for GRCh38 (human)">
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<caption>Human assembly information</caption>
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<tbody>
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<tr>
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<th scope="row">Current major assembly</th>
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<td>GRCh38</td>
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</tr>
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<tr>
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<th scope="row">Regions with alternate loci</th>
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<td>178</td>
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</tr>
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<tr>
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<th scope="row">Assembly N50</th>
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<td>67,794,873 bp</td>
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</tr>
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<tr>
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<th scope="row">Remaining gaps</th>
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<td>875</td>
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</tr>
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<tr>
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<th scope="row">Patch release version</th>
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<td>p14</td>
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</tr>
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<tr>
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<th scope="row">Patches released</th>
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<td><a href="human?filters=type:novel,fix#scaffolds">FIX: 164, NOVEL: 90</a></td>
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</tr>
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</tbody>
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</table>
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<p class="stats_links">More <a href="human/data">human assembly statistics</a>...</p>
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</div>
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</div>
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<div class="spec_info clearfix" id="mouse">
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<div class="critters"><a href="mouse"><img src="/grc/static/grc/img/C57bl6j.png" alt="Mouse" /></a></div>
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<div class="critter_info">
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<h2><a href="mouse">Mouse</a></h2>
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<p>The GRC has produced an updated assembly (GRCm38). This is an update of the last MGSC assembly (MGSCv37) which was described in 2009 (<a href="/pubmed/19468303" target="_blank">PMID: 19468303</a>). The primary assembly is based on assembling overlapping BAC clones derived from the C57BL/6J strain and several loci have sequence available from other strains.</p>
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<table class="brief_stats" summary="Brief stats for GRCm39 (mouse)">
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<caption>Mouse assembly information</caption>
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<tbody>
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<tr>
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<th scope="row">Current major assembly</th>
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<td>GRCm39</td>
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</tr>
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<tr>
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<th scope="row">Regions with alternate loci</th>
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<td>0</td>
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</tr>
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<tr>
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<th scope="row">Assembly N50</th>
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<td>106,145,001 bp</td>
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</tr>
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<tr>
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<th scope="row">Remaining gaps</th>
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<td>347</td>
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</tr>
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<tr>
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<th scope="row">Patch release version</th>
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<td>None</td>
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</tr>
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<tr>
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<th scope="row">Patches released</th>
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<td><a href="mouse?filters=type:novel,fix#scaffolds">FIX: 0, NOVEL: 0</a></td>
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</tr>
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</tbody>
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</table>
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<p class="stats_links">More <a href="mouse/data">mouse assembly statistics</a>...</p>
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</div>
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</div>
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<div class="spec_info clearfix" id="zebrafish">
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<div class="critters"><a href="zebrafish"><img src="/grc/static/grc/img/zebrafish_trans.png" alt="Zebrafish" /></a></div>
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<div class="critter_info">
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<h2><a href="zebrafish">Zebrafish</a></h2>
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<p>The zebrafish genome assembly was produced at the <a href="http://www.sanger.ac.uk/resources/zebrafish/genomeproject.html">Wellcome Sanger Institute</a>. The last assembly produced from the original project was Zv9 and was described in 2013 (<a href="/pubmed/23594743" target="_blank">PMID: 23594743</a>). This assembly is the starting point for the GRC. The assembly is based on assembling overlapping BAC clones and integrating these sequences with the whole genome shotgun assembly.</p>
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<table class="brief_stats" summary="Brief stats for GRCz11 (zebrafish)">
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<caption>Zebrafish assembly information</caption>
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<tbody>
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<tr>
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<th scope="row">Current major assembly</th>
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<td>GRCz11</td>
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</tr>
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<tr>
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<th scope="row">Regions with alternate loci</th>
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<td>607</td>
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</tr>
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<tr>
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<th scope="row">Assembly N50</th>
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<td>7,379,053 bp</td>
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</tr>
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<tr>
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<th scope="row">Remaining gaps</th>
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<td>18,736</td>
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</tr>
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</tbody>
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</table>
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<p class="stats_links">More <a href="zebrafish/data">zebrafish assembly statistics</a>...</p>
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</div>
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</div>
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<div class="spec_info clearfix" id="rat">
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<div class="critters"><a href="rat"><img src="/grc/static/grc/img/FawnHooded_1_Physiogenix_small.png" alt="Rat" /></a></div>
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<div class="critter_info">
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<h2><a href="rat">Rat</a></h2>
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<p>GRCr8 was generated by Dr. Peter Doris (University of Texas Health Science Center at Houston) with colleagues Theodore Kalbfleisch (University of Kentucky) and Melissa Smith (University of Louisville) in the NHGRI-funded "Inbred Rat Genomes Project". The assembly is based on PacBio HiFi sequences from a BN/NHsdMcwi male rat. The assembly was gap filled using contigs from the PacBio CLR reads produced for mRatBN7.2. Additional short read genomic sequence from a BN/NHsdMcwi rat in the Hybrid Rat Diversity Program at the Medical College of Wisconsin were used for assembly polishing.</p>
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<table class="brief_stats" summary="Brief stats for GRCr8 (rat)">
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<caption>Rat assembly information</caption>
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<tbody>
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<tr>
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<th scope="row">Current major assembly</th>
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<td>GRCr8</td>
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</tr>
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<tr>
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<th scope="row">Regions with alternate loci</th>
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<td>0</td>
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</tr>
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<tr>
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<th scope="row">Assembly N50</th>
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<td>137,014,596 bp</td>
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</tr>
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<tr>
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<th scope="row">Remaining gaps</th>
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<td>220</td>
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</tr>
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</tbody>
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</table>
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<p class="stats_links">More <a href="rat/data">rat assembly statistics</a>...</p>
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</div>
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</div>
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<div class="spec_info clearfix" id="chicken">
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<div class="critters"><a href="chicken"><img src="/grc/static/grc/img/Chicken_UCD001.png" alt="Chicken" /></a></div>
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<div class="critter_info">
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<h2><a href="chicken">Chicken</a></h2>
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<p>The chicken genome assembly was produced by the International Chicken Genome Consortium. Gallus_gallus-5.0 is the latest assembly produced from this project. This assembly is the starting point for the GRC. It is comprised primarily of WGS contigs, into which overlapping genomic clones from the same DNA source have been integrated.</p>
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<table class="brief_stats" summary="Brief stats for GRCg6a (chicken)">
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<caption>Chicken assembly information</caption>
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<tbody>
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<tr>
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<th scope="row">Current major assembly</th>
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<td>GRCg6a</td>
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</tr>
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<tr>
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<th scope="row">Regions with alternate loci</th>
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<td>0</td>
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</tr>
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<tr>
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<th scope="row">Assembly N50</th>
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<td>20,785,086 bp</td>
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</tr>
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<tr>
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<th scope="row">Remaining gaps</th>
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<td>946</td>
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</tr>
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</tbody>
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</table>
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<p class="stats_links">More <a href="chicken/data">chicken assembly statistics</a>...</p>
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</div>
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</div>
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</div>
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</div>
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<div class="cleaner"></div>
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<div id="footer">
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<ul>
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<li><a title="Get GRC data via FTP" href="https://ftp.ncbi.nlm.nih.gov/pub/grc/">FTP</a></li>
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<li><a target="_blank" href="https://www.genome.gov">NHGRI</a></li>
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<li><a target="_blank" href="http://www.wellcome.ac.uk">Wellcome Sanger Institute</a></li>
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<li><a target="_blank" href="https://www.hhs.gov">HHS</a></li>
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<li><a target="_blank" href="https://www.nih.gov">NIH</a></li>
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<li><a target="_blank" href="https://www.nih.gov/web-policies-notices">Accessibility</a></li>
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<li class="last"><a target="_blank" href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html">HHS Vulnerability Disclosure</a></li>
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</ul>
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