Type of Notice: Sources Sought
Title: (Source Sought # 12905B24SS0055) – Sources Sought for Genome sequencing of fungal plant pathogens at
USDA-ARS
1636 East Alisal St.
Salinas, CA 93905
Description:
This is a Sources Sought notice Only. This is NOT a solicitation for proposals, proposal abstracts, or quotations. This Sources Sought is issued for information and planning purposes only as part of USDA ARS market research and does not itself constitute an RFQ. This requirement is covered under NAICS code 541714. The purpose of this notice is to obtain information regarding the availability and capability of qualified sources; Small Businesses; HUBZone small business; service-disabled, veteran-owned small business; 8(a) small business; veteran-owned small business; woman-owned small business; or small disadvantaged businesses; Responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible.
The objective is to obtain a contractor who is experienced in two different types of genomic sequencing technologies from a single supplier to generate DNA sequence data from the plant pathogens they work with. Illumina sequencing of a large number of fungal genomes is needed. We also need Oxford Nanopore long read sequencing for genome assemblies. Samples are sent out to a genome sequencing facility.
• Illumina genomic sequence data (150 base pair, paired end data) needs to be generated from a large number of Fusarium oxysporum isolates as part of an external grant funded project (the grant is covering much of the cost of this sequencing). DNA from 80 isolates are submitted at one time for sequencing in a single pooled library. Individual DNA libraries need to be generated and bar coded for each isolate so data can be divided into separate files. The sequencing libraries for all isolates are pooled; each isolate must be carefully quantified so the amount added to the pooled library generates at least 30 million DNA sequencing reads for each isolate. The pooled samples are run on a NovaSeq 6000 platform. It is essential that the highest degree of quality control is followed to prevent cross contamination among the different isolates sequenced in this pool, and from other lanes being run on the equipment. Data needs to be available for download via the internet within 4 weeks.
• Oxford Nanopore long read sequencing – frozen tissue samples are provided for high molecular weight DNA extraction (it is essential that this DNA extraction be done to ensure the highest lengths and purity, and that final DNA sample is compatible with the sequencing technology). A DNA sequencing library is generated and bar coded so sequencing of two isolates can be run in a single R10 flow cell at the same time. The two libraries have to be carefully quantified so when combined for sequencing each isolate will have at least 5 million reads following sequencing on the PromethION platform. It is essential that at least 100,000 of these reads will be over 50 kb in length. It is essential that the highest degree of quality control is followed to prevent cross contamination among the two isolates sequenced in this pool. Data needs to be available for download via the internet within 4-5 weeks.
All datasets found not to be sufficient by the Government will be rerun at no additional cost.
The Government anticipates a Firm Fixed Price contract.
The anticipated start is August 17, 2024
The Government does not intend to make an award based on responses to this inquiry. This notice does not constitute a commitment by the Government.
Capability Statement
All information submitted in response to this announcement is voluntary, and the Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the Government. Business concerns that possess the capabilities necessary to undertake this work should submit complete documentation of their capabilities to the Contracting Officer. Capability statements shall include the Contractors contact point to discuss their response.
The capability statement should include:
1) Acknowledgement that they are able to provide the subject supplies/services being requested;
2) Interested vendors should identify their size standards in accordance with the Small Business Administration;
3) At least three previous requirements that are similar to the requirement include a discussion of the Contract type, delivery method, duration, etc.;
4) Any other information considered relevant to this requirement; and
5) The government requests that no proprietary, classified, confidential, or sensitive information should be included in the response.
Any vendor responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine their qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After review of the responses received, a pre-solicitation synopsis and solicitation may be published on sam.gov depending on the responses received.
All responses to this Sources Sought Notice must be received by the notice’s POC Robert Skipper Robert.skipper@usda.gov and Ted Blume Theodore.Blume@usda.gov by 04:00 PM Central, July 11, 2024 in order to be considered. Responses may not be returned. Responders are solely responsible for all expenses associated with responding to this Inquiry. Do not submit pricing information in response to this Request.
