Specification.docx

Whole Genome Sequencing in Rainbow Trout and Atlantic Salmon

SPECIFICATIONS

The USDA ARS National Cold Water Marine Aquaculture Center (NCWMAC) requires 100x coverage of whole genome sequencing via PacBio RSII and/or PacBio Sequel DNA sequencing systems of one rainbow trout sample (Genome size ~2.5Gb) and one Atlantic salmon sample (Genome size ~3Gb).

Contractor shall provide all services, supplies, equipment and facilities necessary to provide sequencing of two genomic DNA samples (one trout and one Atlantic salmon) in accordance with the required performance elements and benchmarks.

REQUIREMENTS.

1. Amount of DNA provided per sample will be a minimum of 20 ug of high molecular weight rainbow trout or Atlantic salmon genomic DNA. DNA sample QC included: Qubit, 1% agarose gel electrophoresis;

2. Standard PacBio DNA (whole genome) library preparation performed by the vendor following the best practices for whole genome sequencing recommended by PacBio. DNA and Library prep QC: Pulse Field Gel Electrophoresis (PFGE) sizing;

3. Platform and configuration: PacBio RSII and/or PacBio Sequel;

4. Read Length: a smear from short to over 60Kb with N50 of at least 20Kb pass filter reads;

5. Data Output: 250 Gb pass filter reads for the rainbow trout sample and 300 Gb pass filter reads for the Atlantic salmon 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 (see section IV part d).

8. Delivery. The Contractor shall furnish and deliver 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:

9. Documentation. The Contractor shall provide Final Project Report that includes information and documentation on library preparation and Quality Control procedures, documentation of actual fragment sizes used in libraries preps, number of SMRT cells, total output per cell and number of pass filter reads per cell.