STATEMENT OF WORK.docx
DOCX document 16 KB Posted
- Attached to
- Short Read Next Generation Sequencing Federal contract opportunity
- Solicitation number
- 12305B24Q0207
About this file
This document is a Statement of Work for a next generation sequencing project. The primary objective is to use whole genome sequencing to genotype and characterize diversity between 160 eastern oyster broodstock spawned in 2024. The contractor will be required to perform library preparation, paired-end sequencing, and demultiplexing of the 160 samples to generate a minimum of 100 million 150bp paired-end reads per sample. The sequencing data must have at least 70% of bases with a quality score above Q30. The contractor will deliver the sequencing data as FASTQ files within 30 days of sample submission.
The related federal contract opportunity is a Request for Quotation (RFQ) solicitation for this sequencing work. It is a 100% small business set-aside with a NAICS code of 541715 and a 1,000 employee size standard. Quotes are due by September 6, 2024 and the Government intends to award a firm-fixed price contract on a lowest price technically acceptable basis. Offerors must demonstrate technical capability to meet the performance requirements outlined in the Specification Sheet.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| Amendment-01.docx | DOCX document | |
| Terms and Conditions Clauses and Provisions (FAR 2024-05).docx | DOCX document | |
| Wage Determination 2015-4089 rev 27.pdf |
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Text version
Statement of Work Short Read Next Generation Sequencing
BACKGROUND
The USDA ARS NCWMAC Shellfish Genetics program is conducting research on eastern oysters in order to assess genetic diversity and methods of germplasm improvement.
PROJECT OBJECTIVE
The primary objective of this work is to use next generation sequencing (NGS) to genotype and characterize diversity between broodstock spawned in 2024. DNA has been extracted from 160 eastern oysters for whole genome sequencing (WGS). The results of the sequencing will be used by USDA ARS NCWMAC to characterize these 160 individuals and the populations they originated from.
SCOPE OF WORK
The project requires library preparation and paired-end sequencing of 160 samples for WGS. The libraries will be sequenced with 2 x 150 bp reads and target 100 million paired reads per sample (200 million reads total) for a coverage of 50x of a 600 Mbp genome. Sequenced data will be demultiplexed.
DETAILED TECHNICAL REQUIREMENTS
USDA-ARS will submit 160 samples of extracted DNA to the contractor. The contractor will perform construct, and QC whole genome sequencing libraries (one per individual) and sequence these to generate a minimum of 100M 150bp paired end reads (200M reads total, 50x coverage of a 600 Mbp genome) per sample, and demultiplex the sequence data to represent individual samples. Reads for each sample will have a minimum of 70% of bases with quality score above Q30. Sequence data will be collected using a technique that produces minimal insertion/deletion errors, such as the Illumina platform or equivalent. The contractor will deliver the demultiplexed sequence data as FASTQ files to USDA ARS.
DELIVERABLES
The contract will be considered complete upon receipt of demultiplexed sequence data meeting the technical requirements for each sample as well as a brief description of the library preparation protocol (e.g., names of kits and adaptors used) and sequencing instrument (e.g., model name and version) used.
REPORTING SCHEDULE
The sequencing data should be sent to Thomas A. Delomas, USDA ARS NCWMAC Shellfish Genetics, 483 CBLS, 120 Flagg Road, Kingston, RI 02881, or posted on a private server for download within 30 days of sample submission.
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