NFFP71002202628 SOW for RFQ 06292022.pdf

STATEMENT OF WORK

NF-FP7100-22-02628, CB44181

1.0 GENERAL

1.1 BACKGROUND:

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.

1.2 OBJECTIVE: The purpose of this requisition is to obtain high quality next generation sequencing data, as described in the technical specifications.

2.0 TECHNICAL SPECIFICATIONS:

The services required include 217 sample library preparation, quality control (QC) assessment, and whole genome sequencing (WGS) on the Illumina Novaseq platforms; 7 sequencing only lanes on the Illumina NovaSeq; 48 RNA sequencing (RNAseq) sample extraction, library preparation, QC, and sequencing; 6 small RNAseq library prep, QC and sequencing; and 1 PacBio genome sequencing and assembly (<1 Gb genome). Metrics on output and numbers of reads for Illumina sequencing should conform to Q30 greater than 80% (Q30 > 80%).

Whole genome library preparation and sequencing: DNA samples will be submitted in batches of a minimum of 20 samples at a time. DNA library preparation including sample indexing, quality control, and 2x150 bp sequencing at a minimum depth of 2-3x for a 2.5 Gb genome is requested (5-7.5 Gb raw data / sample) is requested.

Illumina NovaSeq sequencing: Sequencing libraries (indexed) will be submitted as a single sample to be sequenced in 2x150 bp format on the Illumina NovaSeqS4, in a single lane. Once sequencing libraries are submitted to the vendor by the NWFSC, quality control and quantitation 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.

Data are to be de-multiplexed by the vendor given user-provided index to library details.

RNA library preparation and sequencing: Tissue samples will be submitted for RNA extraction for standard RNA sequencing, using polyA selection. Library preparation including sample indexing, quality control and sequencing 2x150bp, generating ~350 million paired end reads.

Small RNA sequencing will include library preparation, quality control, and 2x150bp sequencing (~350 million paired end reads) from user-submitted total RNA samples.

PacBio genome sequencing & assembly (<1 Gb genome): A tissue sample will be submitted for high molecular weight DNA extraction sample preparation, library preparation for PacBio HiFi sequencing, and 30 hour PacBio Sequel II sequencing, followed by de novo genome assembly of generated PacBio data. These data will be delivered by external hard drive due to the large size of the data.

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 (or by external hard drive), within 2 months of submitting the samples or libraries for sequencing. Raw Illumina 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.

3.0 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. PacBio raw data is to be delivered in FASTQ or BAM format immediately after sequencing, and the assembly delivered immediately upon completion of assembly. All sequencing must be completed no later than 30 September 2024.

4.0 PERIOD OF PERFORMANCE

30 September 2022 – 30 September 2024

5.0 PLACE OF PERFORMANCE

Offsite at vendor, with data produced transferred to the Northwest Fisheries Science Center.

6.0 TECHNICAL POINT OF CONTACT (TOC):

PROVIDED UPON AWARD

7.0 SECURITY

• Personnel performing work will not work on-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.

8.0 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.

9.0 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.