Low-Coverage Whole Genome Sequencing of Rainbow Trout Samples

Solicitation / RFP / RFQ

This solicitation is a Request for Quote (RFQ) for low-coverage whole genome sequencing of 2,000 rainbow trout samples. The USDA ARS NCCCWA requires genomic DNA extractions from tissue samples and subsequent sequencing using Illumina technology. The contractor will be responsible for providing all necessary services, supplies, equipment, and facilities to perform the sequencing and impute genotypes.

• DNA extractions from fin tissue samples (2,000 units).

• Low-coverage whole genome DNA sequencing of the samples (2,000 units).

• Return of all unused tissue samples to the government.

• DNA quality check using Qubit or equivalent.

• Standard Illumina genomic DNA library preparation (insert size approx. 350bp-450bp).

• Sequencing platform: Illumina technology, PE 150 cycles.

• Read Length: 2 x 150 nucleotides (paired-end).

• Data Output: Minimum of 1.2 Gbases output DNA sequence per sample from 8M quality-filtered non-duplicate paired-end reads (4M reads in each direction). Minimum sequence coverage required for at least 95% of samples.

• Sequence data delivered in standard fastq format.

• Vendor must have procedures for sample management, handling, and high-throughput processing, including quality control steps.

• Deliverables include FASTQ files, unused tissue samples, and a Final Project Report detailing the process and QC.

• Contract Type: Firm-fixed price requirements contract.

• Period of Performance: June 01, 2026 – September 30, 2026 (approximately 122 days).

• Estimated Value: Not specified.

• Proposal or quote submission instructions: Submit pricing for all items. Quotes must include UEI number, address, contact information, and relevant details.

• Evaluation criteria: Award will be made to the offeror representing the best value to the Government using the Highest Technically Rated with a Fair and Reasonable Price evaluation method. Evaluation factors include Technical Approach, Price, and Past Performance.

• Key deadlines or milestones:

  • Samples provided by government: on or before June 01, 2026.
  • Sequencing completion: within 60 days from receipt of samples.
  • Return of deliverables: within 90 days from receipt of samples.
  • Questions due: May 21, 2026, 12 noon EST.
  • Offers held firm for 90 calendar days from receipt date.

• Not specified.

• Attachment 1 contains Statement of Work for Requirement Details.

• Attachment 2 contains Terms and Conditions.

• Service Contract Labor Standards may apply; wage determinations are provided for six possible locations.

• The document includes numerous FAR and AGAR clauses and provisions that bidders must adhere to.

Form / Attachment / Pricing Sheet

This document is a Wage Determination issued under the Service Contract Act (SCA). It establishes the minimum wage rates and fringe benefits required for various occupations performing work on SCA-covered contracts within specific geographic areas in Maine.

• Geographic Scope: Applies to Cumberland, Sagadahoc, and York counties in Maine.
• Occupational Listings: Provides a comprehensive list of job classifications (e.g., Administrative Support, Automotive Service, Health Occupations, Information Technology) with corresponding minimum hourly wage rates.
• Fringe Benefits: Details required fringe benefits, including health and welfare, vacation, and paid holidays. Specific notes address Executive Order 13706 (Paid Sick Leave) and Executive Order 13658 (Minimum Wage).
• Conformance Process: Outlines the procedure for establishing wage rates for occupations not listed in the determination.

Bidders must use this wage determination to ensure their proposed labor costs comply with federal requirements for any SCA-covered services within the specified counties. Failure to comply can lead to penalties. The listed wage rates and benefits are the minimums that must be offered to employees performing work on the contract.

Form / Attachment / Pricing Sheet

This document is a "Wage Determination" issued under the Service Contract Act. It lists the minimum wage rates and fringe benefits required for various occupations performing work on covered federal contracts in Boulder County, Colorado. Bidders must use this information to ensure they are meeting the labor cost requirements for any contract awarded under this solicitation.

• Occupational Listings: Provides a comprehensive list of job titles (e.g., "Accounting Clerk I", "Automotive Mechanic", "Electrician, Maintenance") along with corresponding minimum hourly wage rates and, in some cases, specific footnotes.
• Fringe Benefits: Indicates that fringe benefits are required and are listed separately. The document specifies "HEALTH & WELFARE: $5.55 per hour" and notes additional requirements related to Executive Orders 13706 and 13658.
• Footnotes: Several occupations have numbered footnotes (e.g., 1, 2) that provide additional specific information, such as exemptions for computer employees or details on night pay and Sunday pay differentials.
• Executive Orders: References Executive Order 13706 (Paid Sick Leave) and Executive Order 13658 (Establishing a Minimum Wage for Federal Contractors), outlining their applicability and requirements.
• Conformance Process: Includes instructions on how to request authorization for additional classifications and wage rates if an occupation is not listed in this determination.

This wage determination is critical for bidders to accurately estimate labor costs. Failure to comply with the specified minimum wages and fringe benefits can lead to contract non-compliance. Bidders must ensure their proposed wages and benefits meet or exceed these requirements for all covered service employees.

Form / Attachment / Pricing Sheet

This document is a Wage Determination issued by the U.S. Department of Labor, Employment Standards Administration, Wage and Hour Division. It specifies the minimum wage rates and fringe benefits required for various occupations performing work under Service Contract Act (SCA) covered contracts in the counties of Jerome and Twin Falls, Idaho.

• Occupational Listing: Provides a comprehensive list of job titles, corresponding occupational codes, and the minimum hourly wage rate for each.
• Fringe Benefits: Indicates that fringe benefits are required and follow the occupational listing, though specific fringe benefit amounts are detailed separately.
• Executive Orders: Notes the applicability of Executive Order (EO) 13706 (Paid Sick Leave) and EO 13658 (Minimum Wage), outlining specific requirements and rates for these.
• Vacation and Holidays: Details the minimum paid vacation and holiday entitlements for employees based on years of service and specific holidays.
• Hazardous Pay Differential: Specifies an 8% differential for high-hazard work and a 4% differential for low-hazard work involving ordnance and explosives.
• Uniform Allowance: Outlines requirements for providing and maintaining uniforms, including reimbursement for cleaning costs.
• Conformance Process: Explains the procedure for establishing wage rates for occupations not listed in the determination.

This document is crucial for bidders as it establishes the minimum labor costs that must be factored into their proposals for any contract work performed in the specified geographic area that falls under the Service Contract Act. Bidders must ensure their proposed wages and benefits meet or exceed these requirements to be compliant.

Form / Attachment / Pricing Sheet

This document is a Wage Determination issued under the Service Contract Act (SCA) for the State of California, specifically for the Area of California Counties of San Diego. It lists the minimum wage rates and fringe benefits required for various occupations when performing contract work covered by the SCA.

• Wage Determination Number: 2015-5635, Revision No. 30, dated May 13, 2026.
• Occupational Listings: Provides a comprehensive list of occupations with corresponding codes, titles, and minimum hourly wage rates.
• Fringe Benefits: Indicates that fringe benefits are required and follow the occupational listing. Specific health and welfare benefits are detailed at the end of the document.
• Executive Orders: Notes the applicability of Executive Order (EO) 13706 (Paid Sick Leave) and EO 13658 (Minimum Wage) for federal contractors.
• Conformance Process: Outlines the procedure for requesting authorization of additional classifications and wage rates if an occupation is not listed.

This document is crucial for bidders to understand the minimum labor costs associated with performing services under a federal contract in the specified geographic area. Bidders must ensure their proposed wages and fringe benefits meet or exceed these requirements to be compliant. It directly impacts the cost proposal and overall competitiveness of bids for SCA-covered contracts.

Form / Attachment / Pricing Sheet

This document is a U.S. Department of Labor Wage Determination, specifically for the Service Contract Act, applicable to the area of California Counties of Los Angeles. It lists occupational wage rates and fringe benefits required for various job classifications.

• Occupational Codes and Titles: A comprehensive list of job titles across various sectors (e.g., Administrative Support, Automotive Service, Health Occupations, Information Technology, Mechanics) with corresponding wage rates.
• Fringe Benefits: Indicates that fringe benefits are required and follow the occupational listing. Specific details on Health & Welfare, Vacation, and Holidays are provided in subsequent sections.
• Footnotes: Several occupations have numbered footnotes referencing specific conditions or requirements, such as those for computer employees, air traffic controllers, and hazardous pay differentials.
• Conformance Process: Outlines the procedure for requesting additional classifications and wage rates not listed in the determination.

This document is crucial for bidders to understand the minimum wage and benefit requirements for service contract employees working in the specified geographic area. It directly impacts labor cost estimations for proposals and ensures compliance with federal labor laws. Bidders must ensure their proposed wages and benefits meet or exceed these determined rates.

Form / Attachment / Pricing Sheet

This document is a Wage Determination issued under the Service Contract Act, providing minimum wage and fringe benefit rates for various occupations in Alameda and Contra Costa Counties, California. It serves as a reference for contractors to ensure compliance with labor laws when performing government contracts in this geographic area.

• Lists numerous occupations categorized by general field (e.g., Administrative Support, Automotive Service, Health Occupations, Information Technology).
• Specifies the minimum hourly wage rate for each occupation.
• Indicates that "Fringe Benefits Required Follow the Occupational Listing," meaning specific fringe benefits are tied to each listed job title.
• Includes footnotes for specific occupations (e.g., Computer Employees, Air Traffic Controllers, Weather Observers) detailing special pay rules like night differential, Sunday pay, hazardous pay, and uniform allowances.
• Provides information on paid sick leave requirements under Executive Orders 13706 and 13658.
• Outlines the conformance process for unlisted occupations.

Bidders must review this document to understand the minimum labor costs associated with performing the contract. The listed wage and fringe benefit rates are mandatory for covered employees. Failure to comply can result in penalties. This document is crucial for accurate cost estimation and proposal development to ensure compliance with federal labor laws.

Form / Attachment / Pricing Sheet

This document, "Attachment 2 - Terms and Conditions," provides the detailed terms and conditions applicable to the solicitation for Low-Coverage Whole Genome Sequencing of Rainbow Trout Samples (Solicitation Number 1232SA26Q0416). It outlines the requirements, contract details, and legal clauses that govern the performance of the work.

• Statement of Requirement: Details the need for genomic DNA extractions and low-coverage whole genome sequencing of 2,000 rainbow trout samples.
• Schedule of Items: Lists CLINs for DNA extractions, sequencing, and return of unused samples, with a period of performance from June 01, 2026, to September 30, 2026.
• Technical Data: Specifies requirements for DNA quality checks, library preparation (Illumina technology, PE 150 cycles), data output (minimum 1.2 Gbases per sample), quality control procedures, and sample handling.
• Deliverables: Includes FASTQ format DNA sequence files, unused tissue samples, and a final project report.
• Contacts: Provides points of contact for technical questions (Yniv Palti) and contract concerns (Tucker Davis).
• FAR and AGAR Clauses: Incorporates numerous Federal Acquisition Regulation (FAR) and Agriculture Acquisition Regulation (AGAR) clauses and provisions by reference, covering various aspects of contract performance, compliance, and administration.

This document is critical for bidders as it defines the specific technical requirements, deliverables, timeline, and contractual obligations. Understanding these terms and conditions is essential for accurately estimating costs, developing a compliant proposal, and assessing the feasibility of meeting the government's needs. Bidders must pay close attention to the technical specifications, data output requirements, and the extensive list of incorporated FAR/AGAR clauses, as these will form the basis of the contract.

Statement of Work (SOW)

To perform low-coverage whole genome sequencing of 2,000 rainbow trout samples for the USDA ARS NCCCWA.

• Provide all services, supplies, equipment, and facilities for DNA extractions and whole genome sequencing.

• Perform DNA extractions from 2,000 fin tissue samples.

• Perform low-coverage whole genome sequencing on the 2,000 DNA samples using Illumina technology.

• Return all unused tissue samples to the government.

• DNA quality check using Qubit or equivalent.

• Standard Illumina genomic DNA library preparation with an insert size of approximately 350bp-450bp.

• Sequencing platform: Illumina technology, PE 150 cycles, 2 x 150 nucleotides (paired-end).

• Data Output: Minimum of 1.2 Gbases output DNA sequence per sample from 8M quality-filtered non-duplicate paired-end reads (4M reads in each direction).

• Minimum sequence coverage required for at least 95% of samples.

• Sequence data delivered in standard fastq format.

• Vendor must have procedures for sample management, high throughput processing, and quality control (QC) steps.

• QC procedures must be documented in the final project report, including adaptor sequences and actual DNA insert size.

• Period of Performance: June 01, 2026 – September 30, 2026.

• Tissue samples provided by the government on or before June 01, 2026.

• Sequencing completion: within 60 days from receipt of samples.

• All deliverables required within 90 days from receipt of samples.

• Deliverables include DNA sequence files in FASTQ format, unused tissue samples, and a Final Project Report.

• Data delivery via secure portal download or external hard drives to USDA-ARS-NCCCWA, 11861 Leetown Road, Kearneysville, WV 25430.

• Order number must be included on all documentation and shipments.

• Technical Questions/Delivery: Yniv Palti (yniv.palti@usda.gov, 304-724-8340), USDA-ARS-NEA Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430.

• Contract Concerns: Tucker Davis (tucker.davis@usda.gov), USDA/ARS / Contracting Operations Branch/Acquisition and Property, 310 Highway 26 E., Poplarville, MS 39470.