5ace60775ebe7144aa3473338a032d6f5d3b2010 donnak Thu Mar 6 13:21:20 2014 -0800 Added hg38 announcement. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index f875f51..5c3e4af 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -14,112 +14,178 @@ </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="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> + <hr> + <p> + <font face="courier" size="3"><b>06 March 2014 - + The new GRCh38 Human Genome Browser is here!</b></font> + <p> + In the final days of 2013, the + <a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/" + target="_blank">Genome Reference Consortium</a> (GRC) released the eagerly awaited GRCh38 + human genome assembly, the first major revision of the human genome in more than four + years. During the past two months, the UCSC team has been + hard at work building a browser that will let our users explore the new + assembly using their favorite Genome Browser features and tools. + Today we're announcing the release of a preliminary browser on the GRCh38 + assembly. Although we still have plenty of work ahead of us in constructing the rich + feature set that our users have come to expect, this early release will allow you to + take a peek at what's new. + <p> + Starting with this release, the UCSC Genome Browser version numbers for human + assemblies will match those of the GRC to minimize version confusion. Hence, the GRCh38 + assembly is referred to as hg38 in Genome Browser datasets and documentation. We've + also made some slight changes to our chromosome naming scheme that affect primarily the + names of haplotype chromosomes, unplaced contigs and unlocalized contigs. For more details + about this, see the + <a href="../cgi-bin/hgGateway?db=hg38">hg38 gateway page</a>. + <p> + <b>What's new in GRCh38?</b> + <ul> + <li> + <b>Alternate sequences</b> - Several human chromosomal regions exhibit sufficient + variability to prevent adequate representation by a single sequence. To address this, the + GRCh38 assembly provides alternate sequence for selected variant regions through the + inclusion of <em>alternate loci scaffolds</em> (or <em>alt loci</em>). Alt loci are + separate accessioned sequences that are aligned to reference chromosomes. This assembly + contains 261 alt loci, many of which are associated with the LRC/KIR area of chr19 and the + MHC region on chr6. (See the + <a href="../cgi-bin/hgTracks?chromInfoPage=">sequences</a> page for a complete list of the + reference chromosomes and alternate sequences in GRCh38.) + <li> + <b>Centromere representation</b> - Debuting in this release, the large megabase-sized gaps + that were previously used to represent centromeric regions in human assemblies have been + replaced by sequences from centromere models created by + <a href="http://genome.cshlp.org/content/early/2014/02/05/gr.159624.113.abstract" + target="_blank">Karen Miga et al.</a> of UCSC's + <a href="http://cbse.soe.ucsc.edu/people/kent" target="_blank">Kent lab</a>, under the + guidance and mentorship of the <a href="http://www.genome.duke.edu/labs/WillardLab/" + target="_blank">Willard lab</a> at Duke University. The models, which provide the + approximate repeat number and order for each centromere, will be useful for read mapping + and variation studies. + <li> + <b>Mitochondrial genome</b> - The mitochondrial reference sequence included in the GRCh38 + assembly and hg38 Genome Browser (termed "chrM" in the browser) is the + <a href="http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq" + target="_blank">Revised Cambridge Reference Sequence</a> (rCRS) from + <a href="http://mitomap.org/MITOMAP" target="_blank">MITOMAP</a> with GenBank accession + number J01415.2 and RefSeq accession number NC_012920.1. This differs from the chrM + sequence (RefSeq accession number NC_001907) used by the previous hg19 Genome Browser, + which was not updated when the GRCh37 assembly later transitioned to the new version. + <li> + <b>Sequence updates</b> - Several erroneous bases and misassembled regions in GRCh37 have + been corrected in the GRCh38 assembly, and more than 100 gaps have been filled or reduced. + Much of the data used to improve the reference sequence was obtained from other genome + sequencing and analysis projects, such as the <a href="http://www.1000genomes.org/" + target="_blank">1000 Genomes Project</a>. + <li> + <b>Analysis set</b> - The GRCh38 assembly offers an "analysis set" that was + created to accommodate next generation sequencing read alignment pipelines. Several + GRCh38 regions have been eliminated from this set to improve read mapping. + The analysis set may be downloaded from the Genome Browser + <a href="http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/" + target="_blank">downloads page</a>. + </ul> + <p> + For more information about the files included in the GRCh38 GenBank submission, + see the + <a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/README" + target="_blank">GRCh38 README</a>. The GRCh38 GenBank record provides a detailed + array of <a href="http://www.ncbi.nlm.nih.gov/assembly/883148/#/st_Primary-Assembly" + target="_blank">statistics about this assembly</a>. + Bulk downloads of the sequence and annotation data may be obtained from the Genome + Browser <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#human">Downloads</a> + page. The annotation tracks for this browser were generated by UCSC and collaborators + worldwide. + </p> + <p> + <b>Much more to come!</b> This initial release of the hg38 Genome Browser provides a + rudimentary set of annotations. Many of our annotations rely on data sets from external + contributors (such as our popular SNPs tracks) or require massive computational effort + (our comparative genomics tracks). In the upcoming months/years, we will release many more + annotation tracks as they become available. To stay abreast of new datasets, join our + <a href="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" + target="_blank">genome-announce</a> mailing list or follow us on + <a href="http://www.twitter.com/GenomeBrowser" target="_blank">twitter</a>. + </p> + We'd like to thank our GRC and NCBI collaborators who worked closely with + us in producing the hg38 browser. Their quick responses and helpful feedback were a + key factor in expediting this release. The production of the hg38 Genome Browser was + a team effort, but in particular we'd like to acknowledge the engineering efforts of Hiram + Clawson and Brian Raney, the QA work done by Steve Heitner, project guidance + provided by Ann Zweig, Robert Kuhn, and Jim Kent, and documentation work by Donna + Karolchik. + See the <a href="goldenPath/credits.html#human_credits">Credits</a> page for a detailed + list of the organizations and individuals who contributed to this release. + </p> <p> + <hr> <font face="courier" size="3"><b>04 March 2014 - - Introducing Genome Browser Highlight Feature</b></font> + Introducing new Genome Browser highlight feature</b></font> </p> - We are excited to announce the new highlight feature in the UCSC + We are excited to announce a new highlight feature in the UCSC Genome Browser. Using drag-and-select, you can now highlight a region or gene of interest. <br><br> <img style="border: 2px solid black; margin-left:auto; margin-right:auto; display: block;" src="../images/highlight_screenshot.png" alt="Highlight screenshot"> <br> <p> To highlight a region: Click and hold the mouse button on one edge of the desired area to be highlighted in the Base Position track, drag the mouse right or left to highlight the selection area, then - release the mouse button. Click the "Highlight" button on the - "drag-and-select" popup. More details about this new feature + release the mouse button. Click the "Highlight" button on the + "drag-and-select" popup. More details about this new feature can be found on our - <a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Highlight" - target="_blank">help</a> page. - <P> + <a href="goldenPath/help/hgTracksHelp.html#Highlight" target="_blank">help</a> page. + </p> + <p> Credit goes to Tim Dreszer, Larry Meyer, Robert Kuhn and Luvina Guruvadoo for the design, development and testing of this feature. Additional testing was also provided by several members of the QA team. - - <p> - <font face="courier" size="3"><b>28 February 2014 - - New! Expanded onsite workshop program!</b> </font> </p> <p> - Explore the full power of the UCSC Genome Browser! Thanks to the funding support - of NHGRI, we can now offer hands-on Genome Browser training onsite at your - institution, tailored to your audience's level of expertise. Through this - program, the services of our expert trainer are provided for free, and - participating institutions cover only the transportation from UCSC, lodging, - and a flat fee to cover other costs. - </p> - <p> - For more information or to submit a request for a workshop, please visit - <a href="http://bit.ly/ucscTraining" target="_blank">our survey</a>. - </p> <hr> <!-- staged for archive use <p> <font face="courier" size="3"><b>04 March 2014 - - Introducing Genome Browser Highlight Feature</b></font> + Introducing Genome Browser highlight feature</b></font> </p> - We are excited to announce the new highlight feature in the UCSC + We are excited to announce a new highlight feature in the UCSC Genome Browser. Using drag-and-select, you can now highlight a region or gene of interest. <a href="goldenPath/newsarch.html#030414">Read more</a>. </p> - <p> - <font face="courier" size="3"><b>28 February 2014 - - New! Expanded onsite workshop program!</b> </font> - </p> - <p> - Explore the full power of the UCSC Genome Browser! - Thanks to the funding support of NHGRI, we can now offer hands-on Genome Browser - training onsite at your institution. For more information or to submit a request - for a workshop, please visit <a href="http://bit.ly/ucscTraining" target="_blank">our survey</a>. - </p> - --> - <!-- start archives --> - <p> - <font face="courier" size="3"><b>14 January 2014 - - Two E. coli comparative assembly hubs now available</b></font> - </p> - <p> - We're pleased to add two new assembly hubs produced by the UCSC - <A HREF="https://cbse.soe.ucsc.edu/hausslerlab" TARGET="_BLANK">David Haussler lab</A> - to our collection of publicly available hubs. - <a href="goldenPath/newsarch.html#011414">Read more</a>. - </p> - <p> - <font face="courier" size="3"><b>22 January 2014 - - Web Sequences Track now available for hg19 and other assemblies</b></font> - </p> - <p> - We're pleased to announce the release of the Web Sequences track on the UCSC Genome Browser. This - track, produced in collaboration with Microsoft Research, contains the results of a 30-day scan for - DNA sequences from over 40 billion different webpages. - <a href="goldenPath/newsarch.html#012214">Read more</a>. + <font face="courier" size="3"><b>28 February 2014 - + New! Expanded onsite workshop program!: </b> </font> + Explore the full power of the UCSC Genome Browser! + Thanks to the funding support of NHGRI, we can now offer hands-on Genome Browser + training onsite at your institution. + <a href="goldenPath/newsarch.html#022814">Read more</a>. </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>