Omni-C and RNA Sequence Reads for Pecan & Hickory Species

The Department of Agriculture Agricultural Research Service seeks Omni-C and RNA sequence reads for Pecan and Hickory species, with quotations due July 3, 2026 at 4:00 a.m. Central Standard Time and questions due June 30 at 3:00 a.m. This is an unrestricted acquisition with no set-aside; all responsible sources may quote.

Place of performance is Byron, Georgia. The requirement spans the period July 7, 2026 through March 31, 2027, with delivery to the Sea Fruit and Nut Research facility. The contractor must extract nuclei from leaf tissue samples, construct Omni-C libraries targeting 30x coverage per haplotype with PE150 reads on a genome estimated at 670–800 Mb with 16 chromosomes, sequence approximately 2 million PE 75bp reads for library quality assessment, extract RNA with rRNA depletion, and perform RNA sequencing to approximately 20 million read pairs per sample on an Illumina platform. Work includes scaffolding government-provided draft assemblies to chromosome-scale using Dovetail HiRise software and may include TAD (Topologically Associating Domains) analysis. Deliverables comprise 15 HiRise assemblies in FASTA format with detailed assembly statistics, Omni-C library features, linkage density plots, scaffold break details, BAM files with mapped alignments, and TAD analysis outputs at 10kbp, 25kbp, and 50kbp resolutions, plus 24 pairs of FASTQ files from RNA sequencing with QC reports.

The NAICS code is 541380, Testing Laboratories and Services, with a small business size standard of $19.0 million. Award will be made as a Firm Fixed Price contract to a single offeror on a lowest price technically acceptable basis. Evaluation criteria require quotations to include detailed descriptions of ability to perform, relevant experience providing sequence data to government agencies, and past performance history; quotations offering only the stated specifications without additional substantive information will not be considered. Quotations must be submitted electronically to lynn.hults@usda.gov; faxed or hard copy submissions are not accepted. Vendors must be active and registered in SAM.gov at quotation submission and award. Service Contract Act prevailing wage rates apply.