C04a SOW 1232SA26Q1144 .pdf

Statement of Work

Low-Pass Sequencing

Background

The USDA ARS U.S. National Cotton Germplasm Collection (NPGS-COT) seeks to generate accession-level genomic fingerprints for approximately 576 accessions from the U.S. National

Cotton Germplasm Collection (NPGS-COT) through low-pass whole-genome sequencing.

Objectives

The objective is to generate accession-level genomic fingerprints for approximately 576 accessions from the U.S. National Cotton Germplasm Collection (NPGS-COT) through low-pass whole-genome sequencing.

Scope

The contractor shall provide library preparation, sequencing, and delivery of high-quality genomic data sufficient to achieve an average target coverage of approximately 6.5× per accession. The resulting data will support germplasm identification, accession fingerprinting, population structure analyses, duplicate detection, genomic resource development, and future imputation-based genotyping efforts. The Government seeks a commercially proven and scalable sequencing solution that maximizes data quality, throughput, and cost efficiency while maintaining complete sample traceability and data integrity.

Requirements

The contractor shall:

1. Receive and inventory of genomic DNA samples submitted by the Government

2. Perform DNA quality-control assessments and report any samples failing minimum requirements

3. Prepare sequencing libraries using a high-throughput whole-genome sequencing workflow

4. Sequence approximately 576 cotton accessions using the Nova Seq X platform with paired-end reads and an average target genome coverage of approximately 6.5× per accession

5. Perform standard sequencing quality-control procedures

6. Provide raw sequencing data files, quality reports, and sample manifests

7. Electronically transfer all project deliverables to the Government. All work shall be conducted using established laboratory procedures designed to ensure sample integrity, data quality, and reproducibility throughout the project lifecycle.

Deliverables

The contractor shall receive genomic DNA samples supplied by the Government, perform quality assessment, prepare sequencing libraries, conduct paired-end whole-genome sequencing, and deliver sequencing data that achieves an average genome coverage of approximately 6.5× for each accession.

Deliverables shall include raw sequence files, associated quality-control metrics, sample tracking information, and documentation demonstrating successful completion of sequencing objectives.

Data shall be delivered in industry-standard formats suitable for downstream genomic analyses.

Reporting Requirements

The sequence data should be sent to USDA ARS U.S. National Cotton Germplasm Collection

(NPGS-COT) 2881 F&B Road, College Station, TX 77845.

Other Considerations

Vendors must demonstrate previous experience successfully applying the technique proposed for generations of accession-level genomic fingerprints.

Performance will be measured by successful processing of all submitted samples, achievement of the specified sequencing coverage target, maintenance of sample identity throughout processing, and timely delivery of complete sequencing datasets and associated quality reports.