R--BioNano Mapping

SOURCES SOUGHT: This is a SOURCES SOUGHT NOTICE. The U.S. Geological Survey is conducting a MARKET SURVEY to determine the interest and capability of any firm eligible to compete under NAICS code 541380 with a Small Business Size Standard $16.5M for an upcoming requirement. The Molecular Ecology Laboratory is in the process of constructing de novo genome assemblies for three non-model bird species of conservation concern. Next generation sequencing alone is not enough for the construction of contiguous and accurate genome assemblies. Performing optical mapping helps order and orient sequence fragments, estimate the gap size between adjacent sequences and helps identify and correct potential chimeric joins in the assembly. THIS IS NOT A SOLICITATION. ALL COST ASSOCIATED WITH PROVIDING INFORMATION AS REQUESTED BY THIS SOURCES SOUGHT NOTICE SHALL BE THE RESPONSIBILITY OF THE CONTRACTOR. Submission is voluntary. The scope of work will include: For each species the contractor will perform high molecular weight (HMW) DNA extractions from either whole blood (~400 ul) or tissue and any associated quality control checks. The contractor will use up to 2 enzymes to Nick the sequence motif, Label, Repair, and Stain (NLRS) or use the Direct Label and Stain method (DLS). The DNA will be linearized, and label patterns imaged on either the lrys system or the Saphyr system. The generated data will be combined with next generation sequencing data to produce hybrid scaffolding and final FASTA and AGP files. The contractor shall perform HMW DNA extractions and quality checks for sufficient concentration and purity on submitted samples. The contractor shall use up to 2 enzymes to Nick the sequence motif, Label, Repair, and Stain (NLRS) or use the Direct Label and Stain method (DLS). The DNA will be linearized, and label patterns imaged on either the lrys system or the Saphyr system. The contractor shall combine the generated data with next generation sequencing data to produce hybrid scaffolding and the final sequencing assembly in FASTA and AGP files that are suitable for submission to GenBank. The contractor shall return any unused tissue/blood and extracted DNA to the Molecular Ecology Laboratory. The government will send either frozen tissue (e.g., small amount of muscle tissue) or fresh or frozen whole blood (~ 400 ul) from 3 bird species to the contractor. The government will also provide any associated next generation sequencing data for the three species. For each species, the contractor will provide an updated reference FASTA file and scaffolding information in AGP format that would be acceptable for submission to GenBank. Data files will be made available for download for at least 30 days-after the optical mapping is completed. A statement of work will be provided with any solicitation that may be issued. Responses to this announcement are requested from (1) SBA certified Small Business HubZone firms; (2) Small Business firms certified by a Small Business Administration (SBA) district or regional office for participation in the 8(a) program; (3) Service-Disabled Veteran-Owned small Business firms; (4) Small Businesses. In response to this announcement, please indicate your firm's socioeconomic status (e.g. small business, service-disabled veteran-owned, women owned, HUBZone, etc.) This information will assist the Government in determining how small businesses can fit into the acquisition strategy. A firm is considered small under NAICS code 541380 if their AVERAGE annual receipts for the preceding three (3) years were less than or equal to $16.5 million. Any information submitted is voluntary. If sufficient interest and capability is not received from firms in categories (1) through (4) above, any solicitation may be issued as unrestricted without further consideration. Interested small business firms shall submit (1) NAME, ADDRESS, and PHONE NUMBER OF THE FIRM (including DUNS NUMBER); (2) a CAPABILITY STATEMENT including (a) RECENT (within the last three fiscal years) RELEVANT (similar projects to this requirement) performance history (identify the name of the owner and their point(s) of contact with telephone and fax numbers, e-mail addresses; and (b) in what capacity (e.g., prime, subcontractor etc.) they performed the work; and (3) their SIZE STATUS. Your company must have a DUNs number and be registered on-line at the System for Award Management (SAM). You will also be required to provide your small business status information either via the RFP or the On-line Representations and Certifications (ORCA) also located at the SAM website before an award to your company can be made. Your on-line ORCA registration will cover any/all of your offers to the Federal Government, and only needs updated annually. All responses must be submitted NLT September 3, 2019 at 12:00pm MST via e-mail to: contact@example.gov This is NOT a Request for Proposal (RFP) or Invitation for Bid (IFB) and does not constitute any commitment by the Government. Responses to this sought notice will be used by the Government to make appropriate acquisition decisions. All interested sources must respond to future solicitation announcements separately from responses to this market survey. Any solicitation that may be issued will be posted on the Federal Business Opportunities website and no paper copies will be provided.