Prunus domestica Genome De Novo Assembly

Added: Sep 01, 2017 1:33 pm This is a combined synopsis/solicitation for commercial items prepared under procedures pursuant to the authority of FAR Subpart 13.106 and Part 12 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotations are being requested and a written solicitation will not be issued. Solicitation number AG349BS177659 is being issued as a request for quotation. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-95. This requirement is being conducted as a full and open competition under NAICS 541711. Submission of quotations shall be in accordance with the instructions identified under Item A.5 Instructions for submission of quotation. Companies with the demonstrated technical capability and financial capacity to provide specified services in accordance with the specified Statement of Work delivery schedule are invited

to respond to this request for quote. (A.1) BACKGROUND - The USDA ARS AFRS requires De Novo Assembly of whole Genome Sequencing of Prunus domestica genomic DNA. Contractor shall provide all services, supplies, equipment and facilities necessary to provide deliverables specified in accordance with the terms, conditions, and specifications contained in this document. (A.2) STATEMENT OF WORK - USDA ARS AFRS will provide sufficient quantities of Prunus domestica genomic DNA of sufficient quality for whole genome sequencing. Contractor will provide a de novo assembled, phased, and scaffolded polyploid genome sequence in a standard Fasta format. Minimum N50 scaffold size will be greater than or equal to 1Mbp. Performance Elements and Benchmarks: 1. Verification of DNA quality for DNA submitted. 2. Construction of DNA sequencing libraries using Government provided Prunus domestica genomic DNA and verification of library quality for each of the libraries. Substandard library quality will require library(s) to be reconstructed. 3. Libraries will be subjected to comprehensive sequencing using a combination of synthetic long read and short read sequencing sufficient to produce a phased genome assembly with average coverage of at least 180X. 4. Data quality must at a minimum be the Illumina specification or equal that 80% of the nucleotides are greater than Q30. 5. The complete genome will be assembled in phase to account for subgenomic variation. The assembly must be scaffolded to produce a minimum scaffold size greater than or equal to 1.0 Mbp. 6. Deliverables: The genome sequence will be provided as .fasta files available on a secure site or on a hard drive and shall be provided FOB Destination to USDA-ARS-AFRS 2217 Wiltshire Road, Kearneysville, WV 25430 within 90 days of receipt of quality approved DNA sequencing data. Line Item 01 - Prunus domestica Genome De Novo Assembly $_______ Government Sample will be provided on/before date September 30, 2017. (A.3) INSTRUCTIONS FOR SUBMISSION OF QUOTATION: INSTRUCTIONS FOR SUBMISSION OF QUOTATION - Quotations shall be submitted to the attention of: Timothy Smearman, USDA, AFRS, Administration Office, 2217 Wiltshire Road, Kearneysville, WV 25430 / tim.smearman@ars.usda.gov and be received prior to 4:00 P.M. (EST) on September 11, 2017. ** OFFERORS SHALL SUBMIT THE FOLLOWING: (a) Submit documentation to show technical capability to meet or exceed Performance Elements and Benchmarks. (b) Submit Firm Fixed Price Quotation for each of the Schedule Line Items and Total Price. (c) Submit two separate Past Performance References with contact information for two recent contracts (within past year) of contracts similar to the scope of this requirement of providing a de novo assembled, phased, scaffolded, polyploid genome sequence. To be eligible for an award, contractor must be have current and complete registration in the System for Award Management www.sam.gov. Offeror certifies, by submission of quotation, that registration in SAM is current to include Online Representations and Certifications as of submission date of quotation. Pending availability of funding, the basis for any potential award is Lowest Price Technically Acceptable (LPTA). "LPTA" means the expected outcome of the acquisition that, results from selection of the lowest evaluated price (evaluated as total cost of all line items) technically acceptable quotation that fully meets all specifications and having satisfactory past performance. Only the lowest priced quote will be evaluated for technical acceptability. The next lowest offer will only be evaluated if the aforementioned quote is not found technically acceptable (and so on). Only one award will be made under this solicitation based on availability of funding. The following FAR and AGAR provisions and clauses apply to this acquisition and are available in full text at: http://farsite.hill.af.mil/ 52.204-7 System for Award Management; 52.204-10 Reporting Executive Compensation and First-Tier Subcontract Awards; 52.209-6 Protecting the Government's Interest When Subcontracting with Contractors Debarred, Suspended, or Proposed for Debarment; 52.209-10 Prohibition on Contracting with Inverted Domestic Corporations; 52.211-6 Brand Name or Equal; 52.212-1 Instructions to Offers-Commercial Items; 52.212-2 Evaluation-Commercial Items; 52.212-4 Contract Terms and Conditions - Commercial Items; 52.212-5 Contract Terms and Conditions Required to Implement Statutes or Executive Orders; 52.222-3 Convict Labor; 52.222-19 Child Labor Cooperation with Authorities and Remedies; 52.222-21 Prohibition of Segregated Facilities; 52.222-26 Equal Opportunity; 52.222-36 Equal Opportunity for Workers with Disabilities; 52.222-50 Combating Trafficking in Persons; 52.223-18 Encouraging Contractor Policies to Ban Text Messaging while Driving; 52.225-3 Buy American--Free Trade Agreements--Israeli Trade Act (Alt 2); 52.225-4 Buy American -- Free Trade Agreements - Israeli Trade Act Certificate (Alt 2); 52.225-13 Restrictions on Certain Foreign Purchases; 52.225-25 Prohibitions on Contracting with Entities Engaging in Certain Activities or Transactions Relating to Iran; 52.232-18 Availability of Funds; 52.232-24 Prohibition of Assignment of Claims; 52.232-25 Prompt Payment; 52.232-39 Unenforceability of Unauthorized Obligations; 52.232-33 Payment by Electronic Funds Transfer-System for Award Management; 52.233-1 Disputes; 52.233-3 Protest after Award; 52.233-4 Applicable Law for Breach of Contract Claim; 52.242-13 Bankruptcy; 52.242-17 Government Delay of Work; 52.246-1 Contractor Inspection Requirements; 52.247-34 F.o.b. Destination; 52.249-8 Default (Fixed Price Supply and Service); 52.249-1 Termination for Convenience of the Government (Fixed-Price) (Short Form); 52.252-1 Solicitations Provisions Incorporated by Reference; 52.252-2 Clauses Incorporated by Reference; 452.204-70 Inquiries; 452.219-70 Size Standard and NAICS Code Information.