PACBIO Sequencing Specification_SOW.pdf

PacBio Sequencing for Structural Variants Analysis Whole Genome Sequencing in Rainbow Trout

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 DNA sequencing systems of thirty (30) rainbow trout samples at an average of 10x genome coverage (Genome size ~2.5Gb).

The sequence data will be used for structural genome variants analysis in rainbow trout.

Contractor shall provide all services, supplies, equipment, and facilities necessary to provide sequencing of 30 genomic DNA samples in accordance with the required performance elements and benchmarks.

Schedule of Line Items:

Line Item 01 30 rainbow trout DNA Samples

The rainbow trout DNA samples will be provided to the vendor by December 30, 2021.

REQUIREMENTS.

1. Amount of DNA provided per sample will be a minimum of 5 ug of rainbow trout genomic DNA extracted from fin tissue. DNA samples’ concentration is 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: Pulse Field Gel Electrophoresis (PFGE) sizing;

3. PacBio Sequel DNA sequencing systems to produce long reads using the continuous long reads (CLR) mode;

4. Read Length: N50 of at least 15Kb pass filter reads per sample;

5. Data Output: Average of 25 Gb of pass filter reads 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 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. All data must be provided via secure portal download OR in an external hard drive (including shipping) to the USDA-ARS-NCCCWA.

Completion and return of all deliverables is required within 60 days from receipt of all 30 DNA samples from the government. The order number shall be included on all documentation and shipments.