Attachment 1- Statement of Work.pdf

PacBio HiFi Whole Genome Sequencing of HMW DNA extracted from Rainbow Trout blood samples.

SPECIFICATION

Statement of Work:

The USDA ARS National Center for Cool and Cold-Water Aquaculture (NCCCWA) requires whole genome sequencing via Pacific Biosciences (PacBio) Sequel or Revio DNA sequencing systems of forty eight (48) rainbow trout samples providing at least 10x genome coverage per sample (Genome size ~2.5Gb).

Contractor shall provide all services, supplies, equipment, and facilities necessary to extract high molecular weight (HMW) DNA from rainbow trout blood (fresh in EDTA shipped within 24 hours on ice packs or frozen shipped on dry ice) and provide sequencing of 48 genomic DNA samples in accordance with the required performance elements and benchmarks.

Schedule of Line Items:

Line Item 01 High molecular weight DNA extraction from rainbow trout blood. 48 samples Line Item 02 PacBio HiFi library preparation. 48 libraries.

Line Item 03 HiFi library size selection. 48 libraries.

Line item 04 PacBio Sequel HiFi sequencing of the 48 libraries.

REQUIREMENTS.

1. A minimum amount of 15 ug of rainbow trout HMW genomic DNA extracted by the vendor per blood sample. DNA samples’ concentration will be estimated using Qubit;

2. PacBio DNA (whole genome) library preparation performed by the vendor following the best practices recommended by PacBio. DNA and library prep QC must include HiFi library size selection;

3. PacBio Sequel DNA sequencing systems to produce High Fidelity (HiFi) long reads using the circular consensus sequencing (CCS) mode;

4. Read Length: N50 is at least 12 Kb;

5. Data Output: At least 25 Gb of pass filter reads (>Q20) per sample. The output data files delivered in standard PacBio BAM files format;

6. Vendor must have in place a series of quality control (QC) steps during genomic DNA extractions, libraries preparation and genomic DNA sequencing. Information on library preparation and QC procedures must be documented and included in the final project report, including documentation of the actual fragment sizes used in libraries preps, number of SMRT cells, total output per cell and number of pass filter reads per cell;

7. Deliverables will include the DNA sequencing data for all samples, all raw sequence data files, and Final Project Report. Unused fin tissue samples and unused genomic DNA samples extracted by the vendor will be sent back to the government. All data must be provided via secure portal download OR in an external hard drive (including shipping and handling) to:

ATTN: Dr. Yniv Palti

USDA-ARS-NCCCWA

11861 Leetown Rd Kearneysville, WV 25430

Samples will be provided by the government on or before December 31, 2024. Completion and return of all deliverables is required within 60 days from receipt of all the samples from the government. The order number shall be included on all documentation and shipments.