e7dd9a7b5e82929d1cd81e694a52cf5c6ef89113 luvina Mon Jan 23 09:20:03 2012 -0800 added announcement for wallaby release and compressed bosTau6 announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 3baa6ec..aa2af57 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -14,31 +14,59 @@ </TD></TR></TABLE> </TD></TR></TABLE> <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0> <TR><TH HEIGHT=3></TH></TR> <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> +<!-- Wallaby Assembly release --> + <FONT FACE="courier" SIZE="3"><B>23 January 2012 - Wallaby Browser Available</B></FONT> + <P> + We have released a Genome Browser for the September 2009 + genome assembly of the Tammar Wallaby, <em>Macropus + eugenii</em> (TWGS version Meug_1.1, UCSC version macEug2). This assembly, + which has been sequenced to 2X coverage, was produced by + the Tammar Wallaby Genome Sequencing Consortium, a collaboration + between the <a href="http://www.hgsc.bcm.tmc.edu/project-species-m-Wallaby.hgsc" target="_blank"> + HGSC</a> at Baylor College of Medicine and the + Australian Genome Research Facility Ltd. <a href="http://www.agrf.org.au/default.aspx" target="_blank"></a>. + <P> + Bulk downloads of the sequence and annotation data are + available via the Genome Browser + <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/" target="_blank">FTP server</A> + or the + <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#wallaby" target="_blank">Downloads</A> + page. These data have + <A HREF="credits.html#wallaby_use" target="_blank">specific + conditions for use</A>. + <P> + We'd like to thank the Tammar Wallaby Genome Sequencing Consortium for + providing this assembly. The wallaby Genome Browser and annotation + tracks were produced by Chin Li, Luvina Guruvadoo, and Donna Karolchik. See the + <A HREF="credits.html#wallaby_credits" target="_blank">Credits</A> + page for a detailed list of the organizations and + individuals who contributed to this release. + <P> <FONT FACE="courier" SIZE="3"><B>3 January 2012 - Roadmap Epigenomics Now Available through Data Hub at Washington University</B></FONT> <P> We are pleased to announce the release of the Roadmap Epigenomics data on the UCSC Genome Browser through our Data Hub function. The Roadmap Epigenomics Project is part of The NIH Common Fund's <a href="https://commonfund.nih.gov/epigenomics/" target="_blank">Epigenomics Program</a>. It was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The Consortium leverages experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem @@ -69,79 +97,46 @@ now supports Variant Call Format (VCF). VCF is a flexible and extendable line-oriented text format developed by the 1000 Genomes Project for releases of single nucleotide variants, indels, copy number variants and structural variants discovered by the project. Similar to bigBed, bigWig and BAM, the Browser transfers only the portions of VCF files necessary to display viewed regions, making VCF a fast and attractive option for large data sets. VCF files will need to be compressed and indexed using the tabix package available from <a href="http://samtools.sourceforge.net/" target="_blank">SAMtools</a>. This new format is available for use in custom tracks and data hubs. For more information about VCF and tabix, please see our <a href="goldenPath/help/vcf.html" target="_blank">VCF Track Format help page</a>.</P> <P> + <HR> + + <!-- start archives --> + <!-- bosTau6 Assembly Release --> <FONT FACE="courier" SIZE="3"><B>7 November 2011 - UMD Cow Assembly Now Available in Genome Browser</B></FONT> <P> In response to the many requests from the bovine research community, we now offer the University of Maryland (UMD) <em>Bos taurus</em> assembly in the Genome Browser, in addition to the assemblies produced by the Baylor College - of Medicine Human Genome Sequencing Center. The UMD v3.1 - assembly (Nov. 2009, UCSC bosTau6) was produced by the - <A HREF="http://www.cbcb.umd.edu/" TARGET=_blank>UMD Center - for Bioinformatics and Computational - Biology</A> (CBCB) in College Park, MD. </P> - <P> - The UMD 3.1 assembly is based on reads downloaded from - the NCBI Trace Archive, most of which were sequenced by - the Baylor College of Medicine. UMD reports that they were - able to apply several assembly improvement techniques - to produce an assembly that is substantially more accurate - and complete than previous alternative versions, as - evaluated using independent metrics. Based on UMD - statistics, this assembly provides more genome coverage, - closes thousands of gaps, corrects many erroneous - inversions, deletions, and translocations, and fixes - thousands of single-nucleotide errors. For more information, - see Zimin AV <em>et al</em>, - <A HREF="http://genomebiology.com/2009/10/4/R42" - TARGET=_blank>A whole-genome assembly of the domestic - cow, <em>Bos taurus</em></A>, <em>Genome Biol.</em> 2009;10(4) and - the UMD CBCB - <A HREF="http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml" - TARGET=_blank><em>Bos taurus</em> assembly</A> web page.</P> - <P> - Downloads of the UMD bovine data and annotations may be - obtained from the UCSC Genome Browser - <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/">FTP server</A> - or <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#cow">Downloads</A> page. + of Medicine Human Genome Sequencing Center. + <A HREF="goldenPath/newsarch.html#071111">Read more</A>. </P> - <P> - We'd like to thank the UMD CBCB for providing this genome - assembly. The UMD Cow Genome Browser and annotation tracks - were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg - Roe, Steve Heitner, and Donna Karolchik. See the - <A HREF="goldenPath/credits.html#cow_credits">Credits</A> - page for a detailed list of the organizations and - individuals who contributed to this release. </P> - <P> - <HR> - <!-- start archives --> + <!-- sacCer3 Assembly Release --> <FONT FACE="courier" SIZE="3"><B>10 October 2011 - Updated Yeast Browser Released: </B></FONT> We are happy to announce the release of an updated browser for the <em>Saccharomyces cerevisiae</em> yeast genome. <A HREF="goldenPath/newsarch.html#101011">Read more</A>. </P> <!-- New javascript features --> <P> <FONT FACE="courier" SIZE="3"><B>8 September 2011 - New Navigation and Display Features: </B></FONT> We've added several new features to the Genome Browser that make it easier to quickly configure and navigate around in the browser's annotation tracks window. <A HREF="goldenPath/newsarch.html#090811">Read more</A>.