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JCVI Will Use NGS in Second Phase of Salmon Sequencing Project


The International Cooperation to Sequence the Atlantic Salmon Genome has awarded a contract for next-generation sequencing and analysis to the J. Craig Venter Institute in Rockville, Md.

The contract is the second phase of the project, which aims to develop a reference genome for the Atlantic salmon. A $6 million contract for phase I was awarded to Beckman Coulter Genomics in 2009 to use Sanger sequencing of paired-end, fosmid, and BAC libraries to produce a four-fold coverage genome (IS 12/8/2009).

During the second phase, JCVI will sequence the genome using multiple next-gen sequencing technologies, potentially including both Illumina and 454, according to Mohammed Hasham at Genome British Columbia, who is managing the project for the international consortium.

Other partners in the consortium include the Research Council of Norway, the Norwegian Fishery and Aquaculture Industry Research Fund, and the Chilean Economic Development Agency and its innovation agency InnovaChile.

Additionally, JCVI will integrate the next-gen sequence data with the Sanger sequence data generated by Beckman Coulter to produce an assembly.

The goal is to make the Atlantic salmon genome the most comprehensive of all fish genomes so that it can serve as a reference genome. To accomplish this, the ICSASG has called for a draft genome with contigs that have an N50 of at least 50 kilobases and a quality equivalent to Phred 40 and that can be assembled into scaffolds greater than 1 megabase.

Financial terms of the contract with JCVI were not disclosed.

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