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ISGC Sheep Genome Sequences

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About this Collection

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... more


Genomics


https://doi.org/10.4225/08/51E66EC9696C6


17 Jan 2011


01 May 2013


CSIRO Enquiries
CSIROEnquiries@csiro.au
1300 363 400

sheep whole genome sequence SNP indel


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Link to the Integrative Genome Viewer (IGV) developed at the Broad Institute

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Link to the ISGC Homepage

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Access to the Sheep Reference Genome Assembly v3.1


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. https://doi.org/10.4225/08/51E66EC9696C6


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.

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About this Project

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.


James Kijas


Genome sequencing


Genome sequencing of a diverse collection of sheep and their wild relatives


Experiment


James Kijas


Kim Worley


Hans Daetwyler


Rudi Brauning


Yu Jiang


Brian Dalrymple


Reid Jeffrey


Fuli Yu


Sandra Lee


Yuanqing Wu


Donna M Munzy


Ben Hayes


John McEwan


Shannon Clarke


Anar Khan


Richard Gibbs


Sean McWilliam


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