Chromosome Conformation and Whole Genome Sequencing - KINGSTON RI

Background
The USDA ARS NCWMAC Shellfish Genetics program is conducting research on eastern oysters to assess genetic diversity and develop improved germplasm. This acquisition is set aside for small business concerns, with the applicable North American Industry Classification Standard Code being 541714, and a small business size standard of 1,000 employees.

Work Details
The contractor will perform DNA extraction, library preparation, and paired-end sequencing for two samples for chromosome conformation capture and 21 samples for whole genome sequencing (WGS). All libraries will be sequenced with 2 x 150 bp reads targeting 100 million paired reads per sample (200 million reads total) for a coverage of 50x of a 600 Mbp genome. The contractor must use a non-specific endonuclease or equivalent method for chromosome conformation library preparation, ensuring that over 50% of the cis reads are long-range cis pairs.

The sequence data must have a minimum of 70% of bases with quality score above Q30 and should be collected using techniques that minimize insertion/deletion errors. The contractor will deliver demultiplexed sequence data as FASTQ files to USDA ARS. Additionally, the contract will be considered complete upon receipt of demultiplexed sequence data meeting technical requirements and a brief description of the library preparation protocol within 60 days of sample submission.

Period of Performance
The contract performance period is expected to begin upon award and continue until the completion of deliverables, specifically within the timeline set forth in the solicitation.

Place of Performance
Kingston RI 02881 UNITED STATES

Bidder Requirements
Bidders must demonstrate previous experience successfully applying chromosome conformation library preparation and sequencing techniques to marine invertebrate species. This opportunity is a Total Small Business Set-Aside.