Metagenomic or Shotgun Sequencing
Closed Solicitation Posted
- Solicitation number
- 1232SA26Q0300
- Agency
-
Agricultural Research Service
Department of Agriculture
- Responses due
- Set-aside
- Total Small Business
Opportunity facts
- NAICS code
- 541380 Testing Laboratories and Services
- Place of performance
- Glenside, Pennsylvania 19038, United States
- Points of contact
Notice details come from SAM.gov. Updated .
About this opportunity
The U.S. Department of Agriculture's Agricultural Research Service (USDA ARS) Eastern Regional Research Center (ERRC) is soliciting quotations for metagenomic or shotgun sequencing services under RFQ 1232SA26Q0300. The vendor will perform shallow shotgun sequencing using the Illumina pipeline on 310 DNA samples extracted from bacterial pellets derived from in vitro gut microbiota cultures, divided into two independent shipments (177 samples and 133 samples respectively). Key requirements include DNA library generation with specified fragmentation and barcoding methods, inclusion of negative and positive controls, production of 3-5 million read pairs per sample using a 2x150 base pair configuration, completion of all sequencing and data transfer within 45 days of sample receipt, and performance of all work in the United States. Evaluation will be based on both price and technical capability, with the government reserving the right to select a superior technical solution regardless of price. Questions must be submitted by March 11, 2026 at 1:00 p.m. ET, quotations are due by March 16, 2026 at 5:00 p.m. ET, and quotes must remain valid for a minimum of 60 days.
This is a Total Small Business Set-Aside with a small business size standard of $19 million under NAICS code 541380 (Testing Laboratories and Services), and the solicitation indicates one firm-fixed-price award is anticipated. No incumbent contractor is identified in the available documentation. The estimated contract performance period runs from March 25, 2026 through March 25, 2027, with no specific budget range disclosed in the solicitation materials. Service Contract Act wage rates apply to this procurement, requiring compliance with prevailing wage determinations for Pennsylvania counties including Bucks, Chester, and Montgomery. The place of performance is Glenside, Pennsylvania, and all quotations must include complete pricing that encompasses shipping, data delivery via secure portal, return of unused DNA samples at no additional cost to the government, and all other associated costs.
Notice text
2 versions
Update #2 · Latest ·
Posting has been updated to extend close date and provide additional vendor questions and answers
___________________________________________________________________________________________________
Description
This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR Part 12. This announcement constitutes the only solicitation; offers are being requested, and a separate written solicitation will not be issued.
Solicitation number 1232SA26Q0300 is issued as a Request for Quotation (RFQ) for Metagenomic or Shotgun Sequencing.
This acquisition is set-aside for small business concerns. This solicitation incorporates provisions and clauses by reference. The full text of provisions and clauses may be accessed electronically at www.acquisition.gov.
The applicable North American Industry Classification Standard Code is 541380 Testing Laboratories and Services The small business size standard is $19M This acquisition is a Total Small Business Set-Aside. All responsible sources may submit a quotation which will be considered by the agency.
See “RFQ 1232SA26Q0300” for applicable clauses, instructions, and evaluation criteria.
Statement of Requirement
- ERRC scientists will send extracted DNA from bacterial pellets to be shipped overnight on dry ice for shotgun sequencing. Bacterial pellets will be derived from in vitro culturing of the gut microbiota.
- Important: There will be two shipments of two independent experiments. The first experiment will have 177 samples, and the second experiment will have 133 samples. The total sample number will be 310. The date of the shipments is unknown but will occur within the 12-month period of performance identified in the contract. Once samples are received the vendor will have 45 days to finish the sequencing and transfer the data files.
- After thawing the samples, the vendor will perform metagenomic sequencing (shallow shotgun) using the Illumina pipeline. The Illumina pipeline is required in order to best match previous sequencing data with current sequencing data. I.E. other data generated for this project has been performed using the Illumina pipeline and the current data must be comparable. General steps required for generating the data are listed below. All steps must be performed by the vendor. All steps must be specifically outlined in the provided quote.
- Steps required by the vendor are as follows:
- Generation of the DNA library. Steps include fragmentation of DNA (method of fragmentation must be provided by vendor), the addition of adaptors and molecular barcode indices (specific adaptors and barcodes used must be provided by vendor), and pooling of samples. Quality control of the DNA library must be monitored with DNA quantifications (for example pico green) and/or gel electrophoresis.
- Controls must be included by the company during library prep, both negative and positive. Negative controls include water used during library prep and positive includes DNA from known samples.
- Shallow sequencing will be performed using the Illumina platform. Must produce between 3-5 million read pairs per sample.
- All raw data files will be transferred to scientists at the ERRC. In addition, quality control of raw sequencing reads must be performed which includes demultiplexing, and removal of adaptor sequencing.
- All data generated must be transferred to the USDA within 45 days. Deliverables are listed below.
- All work must be done in the United States to avoid thawing of DNA during shipping.
Award Type
It is anticipated that a firm-fixed price contract will be awarded as a result of this synopsis/solicitation.
The Government intends to make one award from this solicitation. Therefore, to be considered responsive, contractors must submit pricing for all items.
Evaluation and Basis for Award
The provision at FAR 52.212-2, Evaluation—Commercial Products and Commercial Services
is not applicable to this solicitation. In lieu of this provision, quotes will be evaluated in accordance with FAR 12.203 based on the criteria listed below. Award will be made to the offeror representing the best value to the Government.
The Government will conduct a comparative evaluation of quotes to select the Contractor that is best suited to fulfill the requirement. The evaluation factors are: Price and Technical Capability. The Government reserves the right to select a quote that represents a superior technical solution, even if it is not the lowest priced.
Submission Requirements:
To be considered, provide a quote on company letterhead including:
- Vendor Details: SAM.gov UEI Number.
- Technical Documentation: Descriptive material and a "meets/does not meet" statement for the minimum specifications.
- Pricing: Unit price and total price (inclusive of all shipping/delivery costs).
- Timeline: Estimated lead time/delivery date.
- Validity: Quote must be valid for at least 60 days.
Offerors shall identify where the offered item meets or does not meet each of the Government's functional and performance minimum specifications listed herein.
Please ensure all email correspondence includes the solicitation number in the subject line. Emails without the RFQ number in the subject line may not be seen, read, and /or reviewed and therefore disqualified from consideration.
QUESTIONS REGARDING THIS RFQ ARE DUE TO RICHARD HAWTHORNE at Richard.hawthorne@usda.gov, NO LATER THAN 1:00 p. m. ET, March 11th, 2026. Questions will only be accepted via email and WILL NOT be answered if received after this date/time.
QUOTES REGARDING THIS RFQ ARE DUE TO RICHARD HAWTHORNE at Richard.hawthorne@usda.gov , NO LATER THAN 5:00 p. m. ET, March 16th, 2026
Delivery Information
Place of Performance:
USDA - ARS - DAIRY AND FUNCTIONAL FOODS RESE
600 EAST MERMAID LANE
WYNDMOOR PA 19038
Service Contract Labor Standards -
The Service Contract Labor Standards could apply to any contracts awarded through this solicitation. In accordance with (IAW) FAR 22.1002-3(a)(2), the place of performance for this contract is currently known and has included Wage Determinations for the location as an attachment to this solicitation.
A wage determination shall be incorporated in the resultant contract, and there shall be no adjustment to the contract price.
Update #1 ·
Description
This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR Part 12. This announcement constitutes the only solicitation; offers are being requested, and a separate written solicitation will not be issued.
Solicitation number 1232SA26Q0300 is issued as a Request for Quotation (RFQ) for Metagenomic or Shotgun Sequencing.
This acquisition is set-aside for small business concerns. This solicitation incorporates provisions and clauses by reference. The full text of provisions and clauses may be accessed electronically at www.acquisition.gov.
The applicable North American Industry Classification Standard Code is 541380 Testing Laboratories and Services The small business size standard is $19M This acquisition is a Total Small Business Set-Aside. All responsible sources may submit a quotation which will be considered by the agency.
See “RFQ 1232SA26Q0300” for applicable clauses, instructions, and evaluation criteria.
Statement of Requirement
- ERRC scientists will send extracted DNA from bacterial pellets to be shipped overnight on dry ice for shotgun sequencing. Bacterial pellets will be derived from in vitro culturing of the gut microbiota.
- Important: There will be two shipments of two independent experiments. The first experiment will have 177 samples, and the second experiment will have 133 samples. The total sample number will be 310. The date of the shipments is unknown but will occur within the 12-month period of performance identified in the contract. Once samples are received the vendor will have 45 days to finish the sequencing and transfer the data files.
- After thawing the samples, the vendor will perform metagenomic sequencing (shallow shotgun) using the Illumina pipeline. The Illumina pipeline is required in order to best match previous sequencing data with current sequencing data. I.E. other data generated for this project has been performed using the Illumina pipeline and the current data must be comparable. General steps required for generating the data are listed below. All steps must be performed by the vendor. All steps must be specifically outlined in the provided quote.
- Steps required by the vendor are as follows:
- Generation of the DNA library. Steps include fragmentation of DNA (method of fragmentation must be provided by vendor), the addition of adaptors and molecular barcode indices (specific adaptors and barcodes used must be provided by vendor), and pooling of samples. Quality control of the DNA library must be monitored with DNA quantifications (for example pico green) and/or gel electrophoresis.
- Controls must be included by the company during library prep, both negative and positive. Negative controls include water used during library prep and positive includes DNA from known samples.
- Shallow sequencing will be performed using the Illumina platform. Must produce between 3-5 million read pairs per sample.
- All raw data files will be transferred to scientists at the ERRC. In addition, quality control of raw sequencing reads must be performed which includes demultiplexing, and removal of adaptor sequencing.
- All data generated must be transferred to the USDA within 45 days. Deliverables are listed below.
- All work must be done in the United States to avoid thawing of DNA during shipping.
Award Type
It is anticipated that a firm-fixed price contract will be awarded as a result of this synopsis/solicitation.
The Government intends to make one award from this solicitation. Therefore, to be considered responsive, contractors must submit pricing for all items.
Evaluation and Basis for Award
The provision at FAR 52.212-2, Evaluation—Commercial Products and Commercial Services
is not applicable to this solicitation. In lieu of this provision, quotes will be evaluated in accordance with FAR 12.203 based on the criteria listed below. Award will be made to the offeror representing the best value to the Government.
The Government will conduct a comparative evaluation of quotes to select the Contractor that is best suited to fulfill the requirement. The evaluation factors are: Price and Technical Capability. The Government reserves the right to select a quote that represents a superior technical solution, even if it is not the lowest priced.
Submission Requirements:
To be considered, provide a quote on company letterhead including:
- Vendor Details: SAM.gov UEI Number.
- Technical Documentation: Descriptive material and a "meets/does not meet" statement for the minimum specifications.
- Pricing: Unit price and total price (inclusive of all shipping/delivery costs).
- Timeline: Estimated lead time/delivery date.
- Validity: Quote must be valid for at least 60 days.
Offerors shall identify where the offered item meets or does not meet each of the Government's functional and performance minimum specifications listed herein.
Please ensure all email correspondence includes the solicitation number in the subject line. Emails without the RFQ number in the subject line may not be seen, read, and /or reviewed and therefore disqualified from consideration.
QUESTIONS REGARDING THIS RFQ ARE DUE TO RICHARD HAWTHORNE at Richard.hawthorne@usda.gov, NO LATER THAN 1:00 p. m. ET, March 11th, 2026. Questions will only be accepted via email and WILL NOT be answered if received after this date/time.
QUOTES REGARDING THIS RFQ ARE DUE TO RICHARD HAWTHORNE at Richard.hawthorne@usda.gov , NO LATER THAN 5:00 p. m. ET, March 12th, 2026
Delivery Information
Place of Performance:
USDA - ARS - DAIRY AND FUNCTIONAL FOODS RESE
600 EAST MERMAID LANE
WYNDMOOR PA 19038
Service Contract Labor Standards -
The Service Contract Labor Standards could apply to any contracts awarded through this solicitation. In accordance with (IAW) FAR 22.1002-3(a)(2), the place of performance for this contract is currently known and has included Wage Determinations for the location as an attachment to this solicitation.
A wage determination shall be incorporated in the resultant contract, and there shall be no adjustment to the contract price.
Files
| File | Type | Posted |
|---|---|---|
| RFQ 1232SA26Q0300 - MOD 1.pdf | ||
| Additional Questions and Answers.docx | DOCX document | |
| SCA Wage Rates.pdf | ||
| RFQ 1232SA26Q0300.pdf |
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