DNA SEQUENCING

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this Notice. This announcement constitutes the only solicitation: quotes are being requested and written solicitation will not be issued. Solicitation number 12612520Q0006 is issued as a request for quote (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2020-05. This solicitation will be for Full and Open. The associated NAICS code is 541380 , with a size standard $16.5MIL and the PSC code is AZ11. This acquisition is for the following items as identified in the Contract Line Item Whole-genome DNA sequencing of 143 bacterial isolates (each with ~ 5.3 Mb genome size) with ~ 150X average coverage for the purpose of performing de novo assembly. This project will provide the short-read DNA sequencing data for 143 bacterial isolates (each with ~ 5.3 Mb genome size) with ~ 150X average coverage for the purpose of performing de novo assembly, SNP phylogeny, AMR detection/screening, and identify new/novel genes. CONTRACTOR REQUIREMENTS Technical Requirements/Tasks: Provider must perform library preparation, sequencing , and data delivery for DNA samples. Provider must assess/measure the genomic DNA samples provided by the client via a spectrofluorometric assay to ensure that the samples meet quality thresholds. Upon request from the client, provider must be willing to work with samples that do not meet all quality thresholds, including performing any additional purifications necessary to increase the sample quality. Provider must perform fragmentation of genomic DNA samples and size selection to a distribution chosen by the researcher to fit their experimental needs. Provider must prepare samples into uniquely dual-indexed sequencing libraries using a method optimized for creating complex libraries. Provider must assess/measure samples again for quantity and quality, and then pool samples for sequencing. Provider must sequence samples to the custom read length (minimum of paired end 150 bp) and depth (minimum of 5 million reads per sample/isolate) requested by the researcher. Provider must run samples on an Illumina NovaSeq 6000 platform because this platform allows the provider to choose the sequencing depth to any scale that might be required for this project (be it 1 million or 1 billion reads) depending on any changes determined to be necessary after discussions between provider and client to ensure that a minimum of 5 million reads per sample/isolate is achieved. This is necessary given that the genomes for this bacterial species is known to be GC rich and complex with long regions of multiple sequence repeats. Provider must guarantee a Quality score for 2 - 150 bp of ? 75% ? Q30. Provider must transfer all raw data in the form of de-multiplexed FASTQ files and deliver data electronically or via external hard drive upon request of the researcher. Provider must deliver a weekly status report via email by 5:00 pm CT documenting any issues. Purified DNA will be furnished to the provider. Provider will all raw data in the form of demultiplexed FASTQ files via electronic data transfer or via external hard drive upon request of the researcher. You will have 30 business days from the day you receive the DNA Samples to have the DNA Sequencing back to the scientist. The Contractor shall provide all items F.O.B: destination. Location of the Government site is aboard USDA ARS Ames, IA and will be identified in the contract. The Government anticipates award of the Firm Fixed Price Contract. Submitting a Quote: To be eligible for an award, all contractors must be registered in the System for Award Management (SAM) with a current and active registration. A contractor can contact SAM by calling +1 (555) 000-0000 or e-mail at www.sam.gov. NO EXCEPTIONS. A DUNS (Dun and Bradstreet) numbers is required in order to register. Vendor must also include their DUNS # on their quote. Invoices are to be submitted and payments will be made through the IPP system. Vendors must be register or register in the IPP system. Offerors responding to this announcement shall submit their quote on SF-18 (SEE ATTACHED).The quote should include all fees, delivery charges and or surcharges. Only electronic submissions will be accepted. Please email all quotes in writing on the sf-18 to contact@example.gov by no later than May 5, 2020 at 11:00AM Central Standard Time