Sequel Upgrade

Notice of Intent: The USDA, ARS, SEA intends to award a sole source procurement to Pacific Biosciences of California, Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025-1445, as they are the sole source for this type of instrument pursuant to the authority of 41 U.S.C. 253(c)(l ) and FAR 13.106-1(b)(1)(i) Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements. The award will be for the purchase of an upgrade of Pacific Bioscience Sequel I to Sequel System 8M (also known as Sequel II). The existing machine produces ~12 Gbp per cell and produces long read sequences. It can also do circularized reads with impact of greatly increasing read accuracy. PacBio also provide protocols for low input DNA and to date it is the only machine that can produce long reads with low input DNA. As the sole producer and distributor of the Sequel and Sequel II PacBio is the sole source vendor in the USA. Pacific Biosciences is the sole manufacturer and distributor of the Pacific Biosciences Sequel Systems, and their associated library preparation, polymerase, sequencing reagents, and software. The systems are held by numerous patents owned by Pacific Biosciences. PacBio has demonstrated the ability to create high quality genome assemblies from low input DNA without the use of amplification procedures like PCR. Pacific Biosciences Sequel II system can generate high quality DNA sequence from a single insect allowing for de novo genome assembly. Ability to produce quality reads to allow for de novo genome assembly of polyploids like cotton or peanut without additional data from other sources. To generate ~80 billion base pairs per cell with long reads lengths with the ability to have a N50 >25,000 base pairs. To produce high quality and low error reads while still produce read lengths over 10,000 base pairs. Ability to produce high-quality assembly of high- or low-GC content organisms or regions, including highly repetitive regions. Software pipelines specifically for analyzing long-read data provide accurate primary and secondary analysis, especially related to problems with phasing and heterozygosity. The Government intends to award a firm fixed price Purchase Order on or about June 10, 2019, using Simplified Acquisition Procedures. This Notice of lntent is not considered a Request for Quotation (RFQ) nor is it a Request for Proposals (RFP). No solicitation document is available and telephone requests will not be honored. Interested persons may identify their interest and capability to respond to this requirement. A determination by the Government not to compete this proposed contract based on responses to this notice is solely within the discretion of the Government. The Government will consider all responses received by 2:00 PM central time, June 7, 2019. Information received will be considered solely for determining whether to conduct a competitive procurement. Inquiries will only be accepted via email/mail to the Contracting Officer at the following address: Contracting Office Address: Nicholas Langley (CO) USDA-ARS-SEA 1001 Holleman Dr., East, College Station, TX 77840 nicholas.langley@ars.usda.gov Place of Performance: USDA-ARS 141 Experiment Station Road STONEVILLE, Mississippi 38776 Primary Point of Contact.: Jessica Pacheco Contract Specialist jessica.pacheco@ars.usda.gov Secondary Point of Contact.: Nicholas Langley Contract Specialist nicholas.langley@ars.uda.gov