Short Read Next Generation Sequencing
ID: 12305B24Q0207Type: Combined Synopsis/Solicitation
Overview

Buyer

AGRICULTURE, DEPARTMENT OFAGRICULTURAL RESEARCH SERVICEUSDA ARS NEA AAO ACQ/PER PROPBELTSVILLE, MD, 20705, USA

NAICS

Research and Development in the Physical, Engineering, and Life Sciences (except Nanotechnology and Biotechnology) (541715)

PSC

SPECIAL STUDIES/ANALYSIS- SCIENTIFIC DATA (B529)

Set Aside

Total Small Business Set-Aside (FAR 19.5) (SBA)
Timeline
    Description

    The Department of Agriculture, specifically the Agricultural Research Service (ARS), is seeking quotations for a project titled "Short Read Next Generation Sequencing" aimed at library preparation and paired-end sequencing of 160 samples for whole genome sequencing (WGS) of eastern oysters. The selected contractor will be responsible for achieving 100 million paired reads per sample, ensuring a coverage of 50x of a 600 Mbp genome, and delivering high-quality sequencing data in a timely manner. This procurement is critical for advancing the understanding of shellfish genetics and its implications for biodiversity and aquaculture management. Interested small businesses must submit their quotations by September 9, 2024, to Claire Anderson at claire.anderson@usda.gov, and are encouraged to review the attached specification sheet and terms and conditions for compliance requirements.

    Point(s) of Contact
    Files
    Title
    Posted
    The document addresses a specific inquiry about library preparation for PCR (Polymerase Chain Reaction) in relation to an ongoing federal or state RFP process. It clarifies that the use of minimal PCR cycles during library construction is permissible, while a PCR-free protocol is not a requirement. This response is vital for applicants designing proposals involving library preparation, as it outlines acceptable methodologies for project execution. Acceptance of minimal PCR cycles indicates flexibility in the preparation process, potentially influencing how organizations plan and allocate resources for their proposals. Understanding these technical specifications is essential for compliance with the RFP requirements and successful project outcomes within the framework of federal grants and funding initiatives.
    The USDA ARS NCWMAC Shellfish Genetics program aims to assess genetic diversity and improve germplasm of eastern oysters through a next generation sequencing (NGS) project. The initiative focuses on genotyping and characterizing 160 eastern oysters spawned in 2024, utilizing whole genome sequencing (WGS). The scope of work involves library preparation and paired-end sequencing to achieve 100 million paired reads per sample, ensuring a 50x coverage of a 600 Mbp genome. The selected contractor will manage the construction and quality control of the sequencing libraries, and deliver demultiplexed data in FASTQ file format, ensuring high-quality sequencing with a minimum Q30 score for 70% of bases. Completion of the contract hinges on the delivery of sequence data and a brief description of the protocols used. Data is to be submitted to Thomas A. Delomas within 30 days of sample submission, reinforcing timely reporting and detailed technical compliance. This project represents a significant investment in understanding shellfish genetics and its implications for biodiversity and aquaculture management.
    This document outlines the Terms and Conditions for federal contracts under the Federal Acquisition Regulation (FAR) 2024-05, effective May 22, 2024. It encompasses various clauses imperative for contractors dealing with the government, focusing on compliance with legal regulations and safety protocols. Key topics include the prohibition of certain telecommunications and surveillance technologies identified by the Federal Acquisition Supply Chain Security Act (FASCSA), requiring contractors to ensure that no restricted materials are included in their offerings. The document delineates definitions, responsibilities, and compliance requirements for contractors, including searches for covered articles as per FASCSA orders, mandatory reporting of identified restricted items during contract performance, and adherence to specific clauses related to labor standards and ethical practices. Notably, the document emphasizes contractor transparency in disclosure and the obligation to conduct periodic audits of their supply chains. Overall, this framework supports government procurement integrity while reinforcing contractor accountability, safeguarding both national security interests and compliance with labor laws. This guidance is crucial for contractors navigating the complexities of federal bids and grants, ensuring they remain aligned with federal expectations and standards.
    The document outlines the "Register of Wage Determinations" by the U.S. Department of Labor, specifying wage rates for contracts governed by the Service Contract Act. It notes that contracts initiated or extended after January 30, 2022, must pay covered workers a minimum wage of at least $17.20 per hour, while contracts awarded between January 1, 2015, and January 29, 2022, must pay at least $12.90 per hour. The file details applicable wage rates for various occupations, including administrative support, health services, and mechanics, emphasizing compliance with minimum wage standards under Executive Orders 14026 and 13658. Fringe benefits, including health and welfare payments, vacation, and paid holidays, are also detailed. Additional provisions cover paid sick leave as mandated by Executive Order 13706 and uniform allowances for employees required to wear specific attire. The document emphasizes the compliance requirements for contractors and outlines procedures for classifying new job roles not listed in the wage determination, ensuring fair compensation in alignment with the law. This information is vital for government contracts at the federal, state, and local levels, guiding contractors on wage obligations and employee rights.
    Lifecycle
    Title
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    Combined Synopsis/Solicitation
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