2002790 RFQ SOW.docx

STATEMENT OF WORK

NFFP7100-20-02790

PURPOSE:

The NWFSC provides scientific and technical support to NMFS for the management, conservation, and wise use of the Northwest region's marine and anadromous resources. The NWFSC Conservation Biology Division is interested in the conservation of marine species. Obtaining next generation sequencing service is needed to fulfill our research objectives to evaluate genetic diversity in marine organisms, from corals to anadromous salmonids. The purpose of this requisition is to obtain high quality next generation sequencing data, as described in the technical specifications.

TECHNICAL SPECIFICATIONS:

The services required include 12 lanes of Illumina HiSeq3000 or HiSeq4000 (or better) DNA paired end sequencing, 338 sample library preparation, quality control assessment, and whole genome sequencing (WGS) on the Illumina HiSeq 4000 or Novaseq platforms, 24 sample RNA extraction, library preparation, quality control assessment, and RNA sequencing (RNA-seq) on the Illumina HiSeq 4000 or NovaSeq platforms, and 1 sequencing only lane on the Illumina NovaSeq. Metrics on output and numbers of reads should conform to Q30 greater than 80% (Q30 > 80%).

Illumina HiSeq 4000 (or better) sequencing: The sequencing will consist of a minimum sequence length of 150 nucleotides in each read direction (paired end), producing at least 300 million reads per lane (Q30 > 80%). These data must be obtained on the Illumina HiSeq3000/4000 for comparison and use in analyses with data produced from the same instrument in the past. Samples for sequencing will be prepared by Northwest Fisheries Science Center (NWFSC) staff and submitted one, two or three lanes at a time, with a maximum turnaround time of 2 months from sample submission and receipt at the sequencing facility, to delivery of data to the NWFSC. Once sequencing libraries are submitted to the vendor by the NWFSC, quality control of each sample is to be evaluated by the sequencing facility. If samples are low quantity or poor quality as deemed by this QC at the sequencing facility, the sequencing facility shall notify the NWFSC to allow staff at NWFSC to decide whether or not to sequence the library in question.

Whole genome library preparation and sequencing: DNA samples will be submitted in batches of a minimum of 16 samples at a time. DNA library preparation, quality control, and sequencing at a minimum depth of 10x for a 2.5 Gb genome is requested (25 G raw data / sample) is requested.

RNA sequencing sample and library preparation and sequencing: All tissue samples for RNA sequencing will be submitted in a single batch for RNA extraction, RNA QC, RNA-seq library preparation, and sequencing for a minimum of 25 million reads per sample (Q30 > 80%) on the Illumina HiSeq or NovaSeq platforms.

Illumina NovaSeq sequencing: Sequencing libraries will be submitted as a single sample to be sequenced on the Illumina NovaSeqS4, in a single lane. Once sequencing libraries are submitted to the vendor by the NWFSC, quality control of each sample is to be evaluated by the sequencing facility. If samples are low quantity or poor quality as deemed by this QC at the sequencing facility, the sequencing facility shall notify the NWFSC to allow staff at NWFSC to decide whether or not to sequence the library in question.

After sequencing is completed for each set of samples submitted for the above, raw DNA sequence data will be provided to the NWFSC Molecular Genetics laboratory in a format that is downloadable from our user account, within 2 months of submitting the samples or libraries for sequencing. Raw sequencing data shall consist of flat text files containing genetic sequence and quality scores (fastq format), provided by the vendor for each lane of data immediately after sequencing. We analyze the data iteratively as we get each lane of sequencing, each lane informing the next, and once we have reached a target per sample sequence depth, the final run(s) for each project will contain the data we need to do the analysis for our management question.

DELIVERABLE SCHEDULE:

Illumina sequence data is to be delivered as FASTQ files of raw data immediately after sequencing each lane submitted by the NWFSC, and within two months of submission of the sample to the online queue. All sequencing must be completed no later than 30 September 2022.

SECURITY

· Personnel performing work will work primarily off-site.

· Personnel performing work will not require access to NOAA facilities.

· Personnel performing work will not require a PIV or CAC.

· Personnel performing work will not require a NOAA email address.

· Personnel performing work will not require use of DOC owned IT Equipment (Laptop, Desktop Computer).

· Personnel performing work will not require Non-Government IT equipment to interconnect to a DOC network.

· Personnel performing work will not require access to non-public DOC/NOAA data.

DATA PRIVACY

Should work on this agreement require that personnel have access to Privacy information, personnel shall adhere to the Privacy Act, Title 5 of the U.S. Code, Section 552a and applicable agency rules and regulations.

Data created, obtained and collected during the performance of this agreement is the property of NMFS. Data may not be released by any party without written consent from the NMFS POC. Data must be protected from unauthorized disclosure. Personnel must comply with all Federal, DOC, NOAA, and NMFS policies relating to IT and data security.

NON-PERSONAL SERVICE

Personnel performing services under this order will be controlled, directed and supervised at all times by management personnel of the contractor. Personnel will perform independent of and without the supervision of any Government official. Actions of contractor employees may not be interpreted or implemented in any manner that results in any employee creating or modifying Federal policy, obligating the appropriated funds of the U.S. Government, overseeing the work of Federal employees, providing direct personal services to any Federal employee or otherwise violating the prohibitions set forth in Parts 7.5 and 37.1 of the Federal Acquisition Regulations. The NMFS will perform the inspection and acceptance of the completed work.

VENDOR SELECTION

When selecting a vendor, the following will be considered:

Performance Considerations – Performance depends on the vendor having a close working relationship with the staff at the Northwest Fisheries Science Center (NWFSC). This working relationship consists of timely and quick transfer of samples for processing, timely turnaround of data from sequencing, and troubleshooting of anomalous outcomes from sequence data and library preparation. Performance includes important quality control steps to ensure that data received from the vendor are high quality and consistent with the quality and amount of data produced on prior projects in the lab so that data can be integrated.

Successful performance of this contract for services includes quality control of samples received from the NWFSC for Illumina HiSeq4000 or NovaSeq sequencing services (including sample prep, library prep, and QC, as outlined in the statement of work), and high quality data produced from paired end sequencing. The contract also requires that sequencing of samples from the NWFSC can ensue even if only a single sample is received from the NWFSC, by combining lanes for sequencing from multiple libraries received from several independent laboratories. The ability to execute this contract for services depends on the vendor’s mechanism for running samples from multiple labs on different lanes on the Illumina HiSeq and NovaSeq platforms, specific quality control steps for library construction and prior to sample sequencing, and timely delivery of data to the NWFSC.

Technical specifications – The vendor will:

· Conduct quality control on all libraries for sequencing, and communicate QC information to the NWFSC prior to sequencing, so that a decision to sequence the library pending QC results can be made.

· Sequence samples or libraries submitted by the NWFSC on the Illumina HiSeq or NovaSeq platform, producing a minimum amounts of data, as outlined in the Statement of Work.

· Facilitate sample submission, tracking, and data delivery.

· Provide raw data from the instrument in fastq format, downloadable from a password protected website.

· Sequence as few as a single sample from the NWFSC pending enough samples submitted from other sources to run a full flow cell, as per the statement of work.

· Provide raw data from services within 2 months of receipt of the samples.