This is a SOURCES SOUGHT NOTICE ONLY. This is NOT a solicitation for proposals or quotes and does not obligate the Government to award a contract. This notice is for informational and planning purposes only and shall not be construed as a solicitation or an obligation or commitment by the Government, nor is it a Request for Proposal (RFQ) at this time. Responses to this Notice must be in writing.
 

The purpose of this Sources Sought Notice is to conduct market research to determine, in particular, the capability of Small Business firms to provide the supplies/services described below. Documentation of technical expertise must be presented in sufficient detail for the Government to determine that your company possesses the necessary experience to compete for this acquisition. Responses to this notice shall include the following: (a) company name; (b) address; (c) point of contact; (d) email address; (e ) DUNS Number; (f) Cage Code; (g) socioeconomic category (i.e., small business, Service Disabled Veteran Owned Small Business, Veteran Owned Small Business, etc.); (h) a technical/capability statement and; (i) any GSA Schedule numbers.
ARS will accept responses from ALL socioeconomic categories in order to gain a more complete understanding of the market for these services.

The United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Museum of Natural History (NMNH) in Washington, DC has a need for the HiFi PacBio de novo Assembly, Proximity Ligation, RNA Seq Library HiRise Scaffolding, and Basic Genome Annotation Project that will result in a chromosome-level genome assembly of the potato aphid. The data and analyses must be fully reported, repeatable, and reproducible per the following:

– extraction of high molecular weight DNA of an aphid with the average fragment size range of 50-100kb

– DNA QC using 260/280 & 260/230 ratios and obtaining the average fragment size using pulse-field gel electrophoresis

– HiFi PacBio library prep and sequencing to generate ~30X HiFi sequence coverage

– Generate a draft assembly using the hifasm assembler

– Construct one Omnic-C proximity ligation library preparation and sequence ~2M PE75bp reads and map the data back to the draft assembly to assess library quality

– Extract RNA, make an NGS RNA library and perform rRNA depletion

– Generate ~20M 2x150bp RNA-seq reads

– Scaffold the draft assembly through the HiRise software pipeline using the proximity ligation data

– A genome assembly with >70% BUSCO single copy or duplicated score

– Perform whole genome annotation of the genome assembly using RNA-seq data

– ab initio gene prediction using related species

-RNA-seq mapping to enhance annotation – Manual curation of five genes

– Assignment of functional tags to genes

– A report summarizing key assembly statistics, features of the proximity ligation library, and a linkage density plot of the proximity ligation library data

– A table detailing the breaks made in the input scaffolds

– Visualization of structures of manually curated genes

The Period of Performance is estimated Sept 28, 2021 to Sept  27, 2022.  Delivery is to National Museum of Natural History (NMNH), Washington, DC 20560 

The NAICS Code for the expected acquisition is 541714. Any subsequent procurement will be conducted as a commercial item purchase in accordance with FAR Part 12 and as a Simplified Acquisition Procedure in accordance with FAR Part 13.
 

Please email capability statements to Claire Anderson, claire.anderson@usda.gov by 1000 Eastern Time on Tuesday, September 28th, 2021.  Telephone inquiries will not be accepted. Please note “HiFi PacBio Library Prep and Sequencing” in the subject line of the email. 

This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. 

Any organization responding to this notice should ensure that the response is complete and sufficiently detailed to allow the Government to determine the organizations qualifications to deliver the services. Respondents are also advised that the Government is under no obligation to acknowledge receipt of the information or provide feedback about any of the information received. After review of the responses received, the Government may issue a pre-solicitation synopsis and solicitation in Federal Business Opportunities. No proprietary, sensitive, confidential or classified information shall be included with your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation.