06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index afabff9..f45a132 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -10,30 +10,31 @@ <h2>Topics</h2> <ul> <li><a href="#release1">List of UCSC genome releases</a></li> <li><a href="#release2">Initial assembly release dates</a></li> <li><a href="#release3">UCSC assemblies</a></li> <li><a href="#release4">Comparison of UCSC and NCBI human assemblies</a></li> <li><a href="#release12">Differences between UCSC and NCBI mouse assemblies</a></li> <li><a href="#release5">Accessing older assembly versions</a></li> <li><a href="#release6">Frequency of GenBank data updates</a></li> <li><a href="#release7">Coordinate changes between assemblies</a></li> <li><a href="#release8">Converting positions between assembly versions</a></li> <li><a href="#release9">Missing annotation tracks</a></li> <li><a href="#release10">What next with the human genome?</a></li> <li><a href="#release11">Mouse strain used for mouse genome sequence</a></li> +<li><a href="#release13">Looking for a genome assembly?</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a></p> <a name="release1"></a> <h2>List of UCSC genome releases</h2> <h6>How do UCSC's release numbers correspond to those of other organizations, such as NCBI?</h6> <p> The first release of an assembly is given a name using the first three characters of the organism's genus and species classification in the format gggSss#, with subsequent assemblies incrementing the number. Assemblies predating the 2003 introduction of the six-letter naming system were given two-letter names in a similar gs# format and human assemblies are named hg# for human genome.</p> <table border=1> @@ -460,16 +461,56 @@ Rest assured that work will continue. There will be updates to the assembly over the next several years. This has been the case for all other finished (i.e. essentially complete) genome assemblies as gaps are closed. For example, the <em>C. elegans</em> genome has been "finished" for several years, but small bits of sequence are still being added and corrections are being made. NCBI will continue to coordinate the human genome assemblies in collaboration with the individual chromosome coordinators, and UCSC will continue to QC the assembly in conjunction with NCBI (and, to a lesser extent, Ensembl). UCSC, NCBI, Ensembl, and others will display the new releases on their sites as they become available.</p> <a name="release11"></a> <h2>Mouse strain used for mouse genome sequence</h2> <h6>What strain of mouse was used for the Mus musculus genome?</h6> <p> C57BL/6J.</p> +<a name="release13"></a> +<h2>Looking for a genome assembly?</h2> +<p> +When looking for a specific assembly, the best place to start is the <a +href="/cgi-bin/hgGateway">Gateway page</a>. If you begin to type the common species name or +NCBI accession number in the +search box on the left side of the screen, the text will autocomplete if any matches are found. +This search will also match any <a href="/goldenPath/help/hgTrackHubHelp.html#Assembly"> +assembly hubs</a> that are also <a href="/cgi-bin/hgHubConnect">Public Hubs</a>.</p> + +<p> +If there is no match for the assembly on the gateway page, you may search our +<a href="https://hgdownload.soe.ucsc.edu/hubs/">archive of assembly hubs</a>. These include +a large number of NCBI assemblies, as well as Vertebrate Genomes Project assemblies. Note that +many of these are also Public Hubs, and will show up on a <a +href="/cgi-bin/hgGateway">Gateway page</a> search.</p> + +<p> +If the assembly of interest is not found in either location, you may write in to our mailing +list +(<a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>) +including the <a target="_blank" +href="https://www.ncbi.nlm.nih.gov/assembly">NCBI Genbank assembly accession</a> for the requested +assembly in the message. These will start +with either <b>GCA_</b> or <b>GCF_</b>. Our agreement with the genomics community is +that we wait until the assembly has been deposited +into Genbank at NCBI before we process it. See the <a target="_blank" +href="https://www.ncbi.nlm.nih.gov/assembly/docs/submission/"> +Assembly Submission Guidelines page</a> at NCBI for directions on their submission process.</p> + +<p> +Another option available to all users is to create +an <a href="/goldenPath/help/hgTrackHubHelp.html#Assembly"> +assembly hub</a>. These are assemblies created and hosted by users and displayed on the +Genome Browser. This requires no intervention by the UCSC Genome Browser, and can be done for +any assembly. See our <a href="/goldenPath/help/hubQuickStartAssembly.html"> +Quick Start Guide to Assembly Hubs page</a> for additional information and resources. If you +create an assembly hub, consider sharing it with others as a +<a href="/cgi-bin/hgHubConnect">Public Hub</a>. + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->