Friday, March 14, 2014

Fwd: [genome-announce] The new GRCh38 Human Genome Browser has arrived!

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[genome-announce] The new GRCh38 Human Genome Browser has arrived!: "hi all --


In the final days of 2013, the Genome Reference Consortium (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.


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, as well as information about the GRCh38

assembly files, statistics, and links for downloading the UCSC data

files, see the Genome Browser hg38 gateway page

(http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg38).


What's new in GRCh38?


- Alternate sequences - 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 alternate

loci scaffolds (or alt loci). 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.


- Centromere representation - 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regions in human assemblies have been replaced by sequences from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 Karen Miga et al. using centromere

databases developed during her work in the Willard lab at Duke

University and analysis software developed while working in the Kent lab

at UCSC. The models, which provide the approximate repeat number and

order for each centromere, will be useful for read mapping and variation

studies.


- Mitochondrial genome - The mitochondrial reference sequence included

in the GRCh38 assembly and hg38 Genome Browser (termed 'chrM' in the

browser) is the Revised Cambridge Reference Sequence (rCRS) from MITOMAP

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.


- Sequence updates - 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 1000 Genomes Project.


- Analysis set - 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 downloads page.


There's much more to come! 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 genome-announce mailing list or follow

us on twitter.


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.


-Donna

---------------

Donna Karolchik

UCSC Genome Browser Senior Project Manager
http://genome.ucsc.edu


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(Via UCSC-announce.)