A04_Attachment 1-SOW_1232SA26Q0416_Low-Coverage Whole Genome Sequencing of Rainbow Trout Samples.pdf
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- Low-Coverage Whole Genome Sequencing of Rainbow Trout Samples Federal contract opportunity
- Solicitation number
- 1232SA26Q0416
About this file
This is a Statement of Work (SOW) for low-coverage whole genome sequencing services for rainbow trout samples issued by the USDA Agricultural Research Service (ARS) National Center for Cool and Cold Water Aquaculture (NCCCWA).
The contractor shall perform DNA extractions from 2,000 rainbow trout tissue samples stored in 95% ethanol and conduct 0.5x whole genome sequencing using Illumina technology. The work encompasses three line items: (1) DNA extractions from 2,000 fin tissue samples, (2) whole genome low-coverage DNA sequencing from 2,000 DNA samples, and (3) return of all unused tissue samples to the government. The government will provide tissue samples on or before June 1, 2026, with a performance period of June 1, 2026 through September 30, 2026. Sequencing must be completed within 60 days of sample receipt, and all deliverables must be returned within 90 days of receipt.
Required performance elements include DNA quality checks using Qubit or equivalent instruments; standard Illumina library preparation with insert sizes of 350bp-450bp; Illumina PE 150 cycle sequencing with 2 x 150 nucleotide paired-end reads; and minimum data output of 1.2 Gbases per sample from 8M quality-filtered non-duplicate paired-end reads (4M in each direction) for at least 95% of samples. The contractor must deliver DNA sequence files in FASTQ format, a Final Project Report documenting extraction procedures, quality control measures, library preparations, sequencing methodology, and sequence data summaries, and physical return of unused tissue samples. Data delivery shall occur via secure portal download or external hard drives to the USDA-ARS-NCCCWA facility in Kearneysville, West Virginia. The contractor must demonstrate procedures for large-volume sample management and high-throughput processing with documented quality control steps throughout all phases of work.
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Text version
Low-Coverage Whole Genome Sequencing of Rainbow Trout Samples
Statement of Work:
The USDA ARS NCCCWA requires genomic DNA extractions from tissue samples stored in 95% ethanol and 0.5x whole genome sequencing via Illumina technology of 2,000 rainbow trout samples (Genome size ~2.4Gb).
Contractor shall provide all services, supplies, equipment and facilities necessary to sequence and impute genotypes in accordance with the required performance elements and benchmarks.
Schedule of Line Items:
Line Item 01 DNA extractions from 2,000 fin tissues samples
Line Item 02 Whole genome low-coverage DNA sequencing from the 2,000 DNA samples.
Line Item 03 Return of all unused portions of the tissue samples to the government.
Tissue samples will be provided by the government on or before June 01, 2026.
Period of Performance: June 01, 2026 – September 30, 2026
Required performance elements and benchmarks:
1. DNA quality check of all samples using Qubit or other instruments;
2. Standard Illumina genomic DNA library preparation performed by the vendor (Insert size approximately 350bp-450bp);
3. Platform and configuration: Illumina technology, PE 150 cycles;
4. Read Length: 2 x 150 nucleotides (paired-end);
5. Data Output: A minimum of 1.2 Gbases output DNA sequence per sample from 8M quality-filtered non-duplicate paired-end reads (4M reads in each direction). The minimum sequence coverage is required for at least 95% of the samples. The sequence data files are delivered to the government in standard fastq format;
6. Vendor must have in place procedures for management and handling of large volume of samples and high throughput processing of samples. A series of quality control (QC) steps during DNA extractions, libraries preparation and genomic DNA sequencing. The QC procedures must be documented and included in the final project report, including the adaptor sequences used and actual size of DNA inserts;
7. All unused tissue samples must be returned to the government upon completion and acceptance of deliverables by the government.
Attachment 1
Deliverables will include the DNA sequence files in FASTQ format, all unused tissue samples, and a Final Project Report describing DNA extractions, samples QC, library preparations and sequencing, and summary of quantity of sequence data generated per sample and sequence data QC. All data must be provided via secure portal download OR in external hard drives to the USDA-ARS-NCCCWA, 11861 Leetown Road, Kearneysville, WV 25430.
Sequencing should be completed within 60 days from receipt of samples and return of all deliverables are required within 90 days from receipt of samples. The order number shall be included on all documentation and shipments.
Contacts:
• For Technical Questions and/or Delivery Contact:
Technical Point of Contact: Yniv Palti
Email: yniv.palti@usda.gov
Phone: 304-724-8340
Address: USDA-ARS- NEA Cool and Cold Water Aquaculture, 11861
Leetown Road, Kearneysville, WV 25430
• For contract concerns and questions please contact:
Tucker Davis, Contract Specialist
Email: tucker.davis@usda.gov
USDA/ARS / Contracting Operations Branch/Acquisition and Property
Division 310 Highway 26 E., Poplarville, MS 39470
Attachment 1
File details come from the government source that posted it. Updated .