DFFRU Shallow Shotgun DNA Sequencing

Questions and Answers:

Question 1: Exactly how many (extracted) samples will be submitted? The SOW states min 3M reads per sample and the ability to go up to 20M per sample. There’s a difference in cost for 3M vs. 20M reads per sample. Should the bid be based on a min of 3M reads per sample, or 20M reads per sample? If 20M - is that a min of 20M or average of 20M reads per samples?

Answer 1: 3M is minimal requirement, some samples need higher reads, 6M, 13M, 20M, and 40M. The exact number of 3M, 20M, or 40M depend on the nature of experiments. Here is the baseline, if need 3M only, it is 670 sample; if all samples require 20M, it will be 450 sample, and 350 for 40M. Samples from our experiment will have mixed requirements.

Question 2: Regarding user friendly interpretation – we are trying to understand the deliverables so we can price accordingly. Is any functionality required besides alpha diversity or beta diversity measures? Regarding bioinformatics – we are trying to understand the deliverables so we can price accordingly. What specific functional analysis and statistical analysis is required?

Answer 2: Data interpretation will be based on the end-use and guided by end-users. Normally, we ask for taxonomic profiles, bubble charts, sunburst charts, stacked bar charts, unlimited comparative analysis with heat maps, stacked bar charts, matrix tables, alpha diversity, beta diversity, LefSE analysis, and PCA analysis.

Bioinformatics analysis includes functional profiles (metacyc pathways, GO terms, Cazy Enzymes, and pfam., etc.) End of Questions and Answers This is a combined synopsis/solicitation for commercial products or commercial services prepared in accordance with the format in FAR Subpart 12.6, utilizing FAR part 13 procedures, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued.

The solicitation number is 1135285 and this combined synopsis/solicitation is issued as a request for quote (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular FAC 2024-05, dated May 22, 2024. This is a Total Small Business Set-Aside with a NAICS code of 621511 Medical Laboratories and a size standard of $41.5M. The resulting award will be for one (1) firm fixed price line items.

CLIN 0001 will be for one lump sum amount to complete the DNA sequencing as per the Statement of Work (SOW). This is a solicitation to provide shallow shotgun sequencing for hundreds of complex microbial samples in accordance with the SOW. Work must be completed within 60 days of the date of award. FAR Provision 52.212-1, Instructions to Offerors-Commercial Products and Commercial Services, applies to this acquisition.

FAR Provision 52.212-2, Evaluation-Commercial Products and Commercial Services, applies to this acquisition. The Government will award a contract resulting from this solicitation to the responsible offeror whose offer conforming to the solicitation will be most advantageous to the Government, price and other factors considered. The following factors shall be used to evaluate quotes: price, technical capability, and past performance. Technical and past performance, when combined, are less important than price.

Quoters are advised to include a complete copy of FAR Provision 52.212-3, Offeror Representations and Certifications-Commercial Products and Commercial Services. FAR Clause 52.212-4, Contract Terms and Conditions-Commercial Products and Commercial Services, applies to this acquisition.

FAR Clause 52.212-5, Contract Terms and Conditions Required To Implement Statutes or Executive Orders-Commercial Products and Commercial Services, along with the additional FAR clauses cited in the clause as identified in the attached Terms and Conditions, applies to this acquisition. See attached document (Terms and Conditions) for additional requirements, terms, and conditions. Quotes are due Monday, July 29, 2024, 9:00 AM ET. Quotes are to be submitted via email to roger.ammons@usda.gov.

(Must include the Notice ID in the Subject Line) The Contracting Officer, Roger Ammons may be reached at roger.ammons@usda.gov for specific questions regarding this combined synopsis/solicitation. Questions by interested parties regarding the requirement must be submitted by Wednesday, July 24, 2024, by 5:00 PM ET. In order to be considered for award QUOTERS SHALL SUBMIT THE FOLLOWING:

Submit Firm Fixed Price Quote including a technical narrative of how the work will be accomplished, past performance references, total price and valid for at least 60 days after receipt of quote. Submit SAM.gov UEI# with proposal.

REJECTION OF QUOTATION: Failure to demonstrate compliance or to submit all items requested in solicitation will be cause to reject the quote without further discussions.

DISCUSSIONS: The Government intends to award without discussions but reserves the right to conduct discussions should it be deemed in the Government's best interest.