Metagenomic or Shotgun Sequencing

Solicitation / RFP / RFQ

This is a combined synopsis/solicitation (RFQ 1232SA26Q0300) for commercial items, specifically Metagenomic or Shotgun Sequencing services. The acquisition is set-aside for small business concerns. A separate written solicitation will not be issued.

• The vendor will perform shallow shotgun sequencing on extracted DNA from bacterial pellets provided by the ERRC scientists.

• Two shipments of samples are expected, totaling 310 samples (177 in the first, 133 in the second).

• The vendor must use the Illumina pipeline for sequencing to ensure comparability with previous data.

• Required steps include DNA library generation (fragmentation, adaptor/barcode addition, pooling, quality control), inclusion of positive and negative controls, and shallow sequencing to produce 3-5 million read pairs per sample.

• All raw data files must undergo quality control, including demultiplexing and adaptor sequencing removal.

• All generated data must be transferred to the USDA within 45 days of sample receipt.

• All work must be performed in the United States.

• Deliverables include detailed protocols, QC data, adaptor/index information, raw data files via secure portal, demultiplexed data, and return of any leftover DNA.

• Anticipated contract type: Firm-fixed-price.

• Estimated Period of Performance: 03/25/2026 - 03/25/2027 (one year after contract signing).

• Quotes are due by 5:00 p.m. ET on March 16th, 2026.

• Quotes must be on company letterhead and include:

  • Vendor Details (SAM.gov UEI Number)
  • Technical Documentation (descriptive material and "meets/does not meet" statement)
  • Pricing (unit and total, including shipping)
  • Timeline (estimated lead time/delivery date)

• Quotes must be valid for at least 60 days.

• Evaluation factors: Price and Technical Capability. Award will be made to the offeror representing the best value to the Government.

• This acquisition is a Total Small Business Set-Aside.

• Applicable NAICS Code: 541380 (Testing Laboratories and Services).

• Small business size standard: $19M.

• Questions regarding the RFQ are due by 1:00 p.m. ET on March 11th, 2026, and must be submitted via email to Richard.hawthorne@usda.gov.

• All email correspondence must include the solicitation number in the subject line.

• Place of Performance: USDA - ARS - DAIRY AND FUNCTIONAL FOODS RESE, 600 EAST MERMAID LANE, WYNDMOOR PA 19038.

• Service Contract Labor Standards may apply.

Questions & Answers / Clarifications

This document provides clarifications and answers to vendor questions regarding the solicitation for sequencing services.

• Controls: One set of controls per batch is sufficient. Two controls total are required: one positive and one water-only. The specific positive control (e.g., bacterial species) can be determined by the offeror, but information on the control used must be provided.
• Shipping Costs: USDA will pay for sample shipment to the offeror. Offerors must include the cost of shipping remaining DNA back to the USDA in their quote.
• Pricing: Offerors should provide a total price for all contract requirements, not a per-sample unit price. The price of sequencing can vary based on sample numbers and preparation.
• Sample Shipments: Initial 177 samples and subsequent 133 samples will be shipped in single packages, respectively.
• Read Data Volume: The requirement is for 3-5 million read pairs, which equates to 0.9 to 1.5 Gbp of data for a 2x150 bp read configuration.
• DNA Sample Format: Samples will be shipped in a 96-well plate format.
• Library Preparation: While the Illumina sequencing platform is specified, the library preparation kit does not have to be an Illumina brand, as long as it is compatible. The chosen method will be evaluated as part of the quote.

These clarifications refine requirements related to controls, shipping, pricing structure, data volume, and library preparation methods. Offerors should ensure their quotes and proposals address these points accurately.

Solicitation / RFP / RFQ

This is a combined synopsis/solicitation (RFQ 1232SA26Q0300) for Metagenomic or Shotgun Sequencing services. The acquisition is set-aside for small business concerns. The government is procuring services to analyze gut microbial samples.

• Sample Handling: Receive two shipments of bacterial pellets (total 310 samples) on dry ice.

• Sequencing: Perform shallow shotgun sequencing using the Illumina pipeline to generate 3-5 million read pairs per sample. The Illumina pipeline is required for comparability with previous data.

• Library Preparation: Generate DNA libraries, including fragmentation, addition of adaptors and molecular barcode indices, and pooling. Quality control of the library is required.

• Controls: Include negative and positive controls during library preparation.

• Data Transfer: Transfer all raw data files and demultiplexed/adapter-trimmed data to the USDA within 45 days of sample receipt.

• Work Location: All work must be performed in the United States.

• Deliverables: Detailed sequencing protocol, QC data, information on adaptors/indexes, raw data files via secure portal, demultiplexed/adapter-trimmed data, and return of any leftover DNA.

• Contract Type: Anticipated firm-fixed-price contract.

• Period of Performance: One year, estimated 03/25/2026 - 03/25/2027.

• Submission Deadline: Quotes are due by 5:00 p.m. ET on March 12th, 2026.

• Submission Requirements: Quotes must include Vendor Details (SAM.gov UEI), Technical Documentation (descriptive material and "meets/does not meet" statement), Pricing (unit and total, including shipping), and Timeline (estimated lead time/delivery date). Quotes must be valid for at least 60 days.

• Evaluation Criteria: Award will be made to the offeror representing the best value to the Government, based on a comparative evaluation of Price and Technical Capability. The government may select a superior technical solution even if not the lowest priced.

• This acquisition is a Total Small Business Set-Aside.

• Applicable NAICS Code: 541380 (Testing Laboratories and Services).

• Small business size standard: $19M.

• Questions regarding the RFQ are due by 1:00 p.m. ET on March 11th, 2026, to Richard.hawthorne@usda.gov.

• Place of Performance: USDA - ARS - DAIRY AND FUNCTIONAL FOODS RESE, 600 EAST MERMAID LANE, WYNDMOOR PA 19038.

• Service Contract Labor Standards may apply.

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, under the Service Contract Act. It establishes the minimum wage rates and fringe benefits required for various occupations performing work on federal service contracts within a specified geographic area.

• Occupational Codes and Titles: Lists specific job titles and corresponding codes.
• Minimum Wage Rates: Specifies the hourly wage rate for each listed occupation.
• Fringe Benefits: Indicates that fringe benefits are required and follow the occupational listing (details on specific benefits like Health & Welfare are provided later in the document).
• Geographic Area: Applies to Pennsylvania Counties of Bucks, Chester, and Montgomery.
• Executive Orders: Notes the applicability of Executive Order 13706 (Paid Sick Leave) and Executive Order 13658 (minimum wage adjustments).
• Conformance Process: Outlines the procedure for classifying and determining wage rates for occupations not explicitly listed.

This document is crucial for bidders to understand the labor costs associated with performing the contract. It dictates the minimum wages and benefits that must be paid to employees working on the contract, directly impacting the cost proposal. Bidders must ensure their proposed wages and benefits meet or exceed these requirements. The document also provides guidance on how to handle unlisted occupations through the conformance process.