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ISGC Sheep Genome Sequences
The collection contains the genome sequence of a diverse collection of sheep. For each animal, sequence reads are available to a depth of approximately 10 fold genome coverage. Sequence reads are made available in BAM format. Sequence polymorphisms are made available in VCF format following comparison of each animal’s sequence to the sheep re... moreference genome assembly (v3.1). To assist users with interpretation of the collection, the reference genome (FA format) and genome feature files (GFF3 format) are included for viewing using software such as the Integrative Genome Viewer (IGV). less
17 Jan 2011
01 May 2013
whole genome sequence
Sequence reads of each animal were generated using Illumina sequencing of short (200 – 300 bp) insert libraries. Alignment for sequence reads was performed against the sheep reference genome assembly (v3.1) using bwa to create BAM files. Aligned reads were used for variant detection using two independent pipelines; AtlasSNP and SamTools. Only variants independently identified using both pipelines were made available.
The collection was generated under the auspices of the International Sheep Genomics Consortium (ISGC) in a project coordinated by CSIRO. DNA samples were made available by ISGC participants for the benefit of the sheep research community. Data generation was performed at the Baylor College of Medicine’s Human Genome Sequencing Center under the guidance of Kim Worley. The correct genetic identity of each data set was determined by Mike Heaton at the USDA Meat Animal Research Center. Variant calling was performed at 1) the Baylor College by Kim Worley and her team and 2) the Department of Primary Industries Victoria by Hans Daetwyler and Ben Hayes. The final set of variants was defined at AgResearch under the guidance of John McEwan and Rudi Brauning. The sheep reference genome (v3.1) was developed at CSIRO by Brian Dalrymple, Jiang Yu and James Kijas.
CSIRO Data Licence
AgResearch, New Zealand (Australia), Baylor College of Medicine (United States), CSIRO (Australia), DPI, Victoria (Australia), International Sheep Genomics Consortium (Australia), USDA (United States)
Kijas, James; Worley, Kim; Daetwyler, Hans; Brauning, Rudi; Jiang, Yu; Dalrymple, Brian; Jeffrey, Reid; Yu, Fuli; Lee, Sandra; Wu, Yuanqing; Munzy, Donna M; Hayes, Ben; McEwan, John; Clarke, Shannon; Khan, Anar; Gibbs, Richard; McWilliam, Sean (2013): ISGC Sheep Genome Sequences. v2. CSIRO. Data Collection.
All Rights (including copyright) AgResearch, New Zealand, Baylor College of Medicine, USA, CSIRO Australia, DPI, Victoria, International Sheep Genomics Consortium, USDA 2013.
The metadata and files (if any) are available to the public.
CLSD 1206.1 NextGenBreedOpt C2012/5905
The project collected SNP genotypes from a diverse collection of teh world's sheep breeds, before performing analysis to reveal high levels of historic mixture and strong recent selection.
Genome sequencing of a diverse collection of sheep and their wild relatives
Donna M Munzy
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