Titanium Sequencing and Library Prep

This is a combined synopsis/solicitation for the following requirement for U.S. Department of Agriculture, Agriculture Research Service, prepared in accordance with the format in FAR Subpart 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation, offers are being requested aand a written solicitation shall not be issued. USDA, ARS intends to procure the following items or equivalent from the manufacturer and vendor: MOgene, LC, located at 4633 World Parkway Circle. St. Louis, MO 63134 at phone number: 314-824-1931. Line Item 1: Shotgun library prep for Acholeplasma Palmae and Spiroplasma Kunkelii bacterial gDNA, Quantity of 2 each; Line Item 2: 3Kb-paired-end library prep for Acholeplasma Palmae and Spiroplasma Kunkelii bacterial gDNA , Quantity of 2 each; Line Item 3: 8Kb-paired-end library prep for Acholeplasma Palmae and Spiroplasma Kunkelii bacterial gDNA , Quantity of 2 each; Line Item 4: 20Kb-paired-end library prep for Acholeplasma Palmae and Spiroplasma Kunkelii bacterial gDNA, Quantity of 2 each; Line Item 5:1/8 region 454 Titanium Sequencing Runs, Quantity of 8 each; Line Item 6: Analysis - Assembly using Newbler software, Quantity of 2 each; Line Item 7: Data delivery on external hard drive, Quantity of 1 each. The minimum requirements in the above seven lined items or equivalent are as followed: Line Item 1: Preparation of two (2) libraries of sheared and sized DNA, one library consisting of DNA fragments (ca. 500 bp - 800 bp in size) representing the entire genome of the subject organism, Spiroplasma kunkelii, and the other library consisting of DNA fragments (ca. 500 bp - 800 bp in size) representing the entire genome of the subject organism, Acholeplasma palmae. The quality of the DNA fragments will be sufficiently high to allow accurate nucleotide sequencing of the fragments; Line Item 2: Preparation of two (2) libraries of sheared and sized DNA, one library consisting of DNA fragments (ca. 3 kbp in size) representing the entire genome of the subject organism, Spiroplasma kunkelii, and the other library consisting of DNA fragments (ca. 3 kbp in size) representing the entire genome of the subject organism, Acholeplasma palmae. The quality of the DNA fragments will be sufficiently high to allow accurate nucleotide sequencing of the fragments; Line Item 3: Preparation of two (2) libraries of sheared and sized DNA, one library consisting of DNA fragments (ca. 8 kbp in size) representing the entire genome of the subject organism, Spiroplasma kunkelii, and the other library consisting of DNA fragments (ca. 8 kbp in size) representing the entire genome of the subject organism, Acholeplasma palmae. The quality of the DNA fragments will be sufficiently high to allow accurate nucleotide sequencing of the fragments; Line Item 4: Preparation of two (2) libraries of sheared and sized DNA, one library consisting of DNA fragments (ca. 20 kbp in size) representing the entire genome of the subject organism, Spiroplasma kunkelii, and the other library consisting of DNA fragments (ca. 20 kbp in size) representing the entire genome of the subject organism, Acholeplasma palmae. The quality of the DNA fragments will be sufficiently high to allow accurate nucleotide sequencing of the fragments; Line Item 5: Titanium sequencing of both ends of DNA fragments included in the eight (8) DNA libraries specified in the line items 1 through 4, with minimal coverage of 20X per base position for single copy genes, achieved through nucleotide sequencing employing 1/8 titanium plate per library. If sequencing is unsuccessful or unsatisfactory, the above operations in line items 1 through 4 will be repeated; Line Item 6: Assembly of two entire genomes of the subject organisms, Spiroplasma kunkelii and Acholeplasma palmae, from the sequencing reads from all of the above-mentioned DNA fragment libraries. This step will serve as a quality control on the previous steps. If assembly is unsuccessful or unsatisfactory, the above operations in line 5, line items 1 through 4, or line items 1 through 5 will be repeated to achieve satisfactory assembly; Line Item 7: Transfer of original sequencing reads from item 5 and of the assembled genome sequences from line item 6, to USDA. All quotes shall be emailed to: John.Wilkinson@ars.usda.gov; no later than August 29, 2010. All responses shall be evaluated in order to determine the ability to meet the above stated capabilities. The Government intends to award an order resulting from this combined synopsis/solicitation to the responsive/responsible offeror. The anticipated award date is August 30, 2010.