63bd069141e86d8b02dca271e55b2cdb25245522 kuhn Tue Jul 28 16:51:56 2020 -0700 added SARS-CoV-2 to release log. updated blurb abt chrMT diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index faf2e5d..a3aec5d 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -280,30 +280,31 @@ <tr><td></td><td>ce2</td><td>Mar. 2004</td><td>WormBase v. WS120</td><td>Available</td></tr> <tr><td></td><td>ce1</td><td>May 2003</td><td>WormBase v. WS100</td><td>Archived</td></tr> <tr><td><em>C. japonica</em></td><td>caeJap1</td><td>Mar. 2008</td><td>WUSTL 3.0.2</td><td>Available</td></tr> <tr><td><em>C. remanei</em></td><td>caeRem3</td><td>May 2007</td><td>WUSTL 15.0.1</td><td>Available</td></tr> <tr><td><em></em></td><td>caeRem2</td><td>Mar. 2006</td><td>WUSTL 1.0</td><td>Available</td></tr> <tr><td><em>P. pacificus</em></td><td>priPac1</td><td>Feb. 2007</td><td>WUSTL 5.0</td><td>Available</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>OTHER</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td>Sea Hare</td><td>aplCal1</td><td>Sep. 2008</td><td>Broad Release Aplcal2.0</td><td>Available</td></tr> <tr><td>Yeast</td><td>sacCer3</td><td>April 2011</td><td>SGD April 2011 sequence</td><td>Available</td></tr> <tr><td></td><td>sacCer2</td><td>June 2008</td><td>SGD June 2008 sequence</td><td>Available</td></tr> <tr><td></td><td>sacCer1</td><td>Oct. 2003</td><td>SGD 1 Oct 2003 sequence</td><td>Available</td></tr> <tr><td><strong></strong></td><td></td><td></td><td></td><td></td></tr> <tr><td><strong>VIRUSES</strong></td><td></td><td></td><td></td><td></td></tr> <tr><td>Ebola Virus</td><td>eboVir3</td><td>June 2014</td><td>Sierra Leone 2014 (G3683/KM034562.1)</td><td>Available</td></tr> + <tr><td>SARS-CoV-2</td><td>wuhCor1</td><td>Jan. 2020</td><td>SARS-CoV-2 ASM985889v3</td><td>Available</td></tr> </table> <a name="release2"></a> <h2>Initial assembly release dates</h2> <h6>When will the next assembly be out?</h6> <p> UCSC does not produce its own genome assemblies, but instead obtains them from standard sources. Because of this, you can expect us to release a new version of a genome soon after the assembling organization has released the version. A new assembly release initially consists of the genome sequence and a small set of aligned annotation tracks. Additional annotation tracks are added as they are obtained or generated. Bulk downloads of the data are typically available in the first week after the assembly is released in the browser.</p> <a name="release3"></a> @@ -360,31 +361,34 @@ <a name="release4"></a> <h2>Comparison of UCSC and NCBI human assemblies</h2> <h6>How do the human assemblies displayed in the UCSC Genome Browser differ from the NCBI human assemblies?</h6> <p> Human assemblies displayed in the Genome Browser (hg10 and higher) are near identical to the NCBI assemblies when it comes to primary sequence. Minor differences may be present, however. Sources include:</p> <ul> <li>NCBI genomes are repeat masked with RepeatMasker, however, UCSC genomes are independently masked with both RepeatMasker (with different flags) and WindowMasker, ultimately using the program output with the highest percentage masked for the base sequence</li> <li>In genome download files, UCSC uses the 'chr1' nomenclature for sequence identifiers, whereas the primary NCBI sequence identifiers are RefSeq accessions</li> - <li>The mitochondrion for hg19 differs from the one in NCBI (GRCh37)</li> + <li>The original mitochondrion (chrM) for hg19 differs from the one in NCBI (GRCh37)</li> + <li>The mitochondrion released by NCBI after the hg19 browser was built has been added to + the assemby as chrMT. See our <a href = "FAQgenes.html#mito" + target = _blank>documentation</a> for details.</li> </ul> <a name="release12"></a> <h2>Differences between UCSC and NCBI mouse assemblies</h2> <h6>Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?</h6> <p> The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). NCBI provides data for several additional strains in their builds.</p> <a name="release5"></a> <h2>Accessing older assembly versions</h2> <h6>I need to access an older version of a genome assembly that's no longer listed in the Genome Browser menu. What should I do?</h6>