SPECIAL NOTICE
B -- Notice of Intent to Sole Source Dovetail Genomics DNA Sequencing Service
- Notice Date
- 8/2/2016
- Notice Type
- Special Notice
- NAICS
- 541690
— Other Scientific and Technical Consulting Services
- Contracting Office
- Agricultural Research Service - Western Business Service Center
- ZIP Code
- 00000
- Solicitation Number
- AG-4431-S-16-0021
- Archive Date
- 8/24/2016
- Point of Contact
- Shalunda S. Mix, Phone: 662-686-5346
- E-Mail Address
-
shalunda.mix@ars.usda.gov
(shalunda.mix@ars.usda.gov)
- Small Business Set-Aside
- Total Small Business
- Description
- The U.S. Department of Agriculture, ARS, WBSC, Stoneville, Mississippi, intends to award a sole source procurement to Dovetail Genomics, LLC, 2161 Delaware Ave. St. Santa Cruz, CA 95060 for genomic DNA sequencing services for three insects for the purpose of insect growth inhibitor research. The following services will be provided by Dovetail Genomics: Library preparation and scaffolding of genomic sequencing data for the lesser grain borer, yellow mealworm, and rice weevil. QC of customer DNA sample to ensure that DNA will be approximately in the range of 50-150 kbp in length, and that the sample is of high enough purity and concentration for library prep. Dovetail will QC the customer's draft assembly to ensure that the draft assembly meets minimum requirements for scaffolding with HiRise. Construction of proprietary Chicago DNA libraries from the customer's DNA sample. Chicago libraries are able to span distances up to the length of the longest molecule in the DNA sample. A typical sample will contain molecules up to ~150kbp. Hence, we can construct reads that span up to 150kbp. Dovetail will QC the resulting Chicago library to ensure the library has adequate complexity, that the insert distribution meets expectations, and will also calculate how much sequencing is required to reach the target physical coverage of 100X. Upon completion of the Chicago library preparation, Dovetail sequences a small number of read pairs (~1-2 million pairs) from the library and aligns them to the draft assembly. Dovetail uses these alignments to examine the complexity of the library, read pair separation distribution, and signal: noise levels. The library will pass QC if it is predicted to be able to produce greater than 50X physical coverage of the genome with reasonable levels of sequencing. If the library passes both this and the prior QC, then it is ready for deep sequencing. Dovetail will sequence the Chicago libraries with an Illumina HiSeq 2500 using 100bp paired end reads, and to a depth that provides a physical coverage of 100X. Dovetail will run its proprietary scaffolding bioinformatics package, HiRise. HiRise requires a draft genome assembly (that will be provided by the customer), the Chicago sequencing data and the sequencing data from the draft assembly. HiRise will scaffold the genome, typically producing a scaffold N50 of at least 1Mb. After running through the HiRise pipeline, the resulting assemblies are checked against historical results to ensure that the scaffolding is performing as expected. If an assembly passes this checkpoint it is then delivered to the customer. Final deliverables to the customer will include: •The final HiRise assembly in FASTA format •A table detailing the breaks made to the input scaffolds •A table describing the position of the input assembly scaffolds within the final HiRise scaffolds •BAM files containing Chicago read data mapped to the input assembly, as well as the unmapped reads •QC reports Terms: Chicago Method: Dovetail's proprietary, in vitro, long-range sequencing library preparation method. Chicago Library: A sequencing library produced by the Chicago method. Library Complexity: The estimated number of unique molecules within a sequencing library. HiRise: Dovetail's internally developed genome scaffolding software pipeline. Input or Draft assembly: The assembly to be scaffolded by the HiRise pipeline using Chicago data. Contig: A contiguous assembled fragment within a genome assembly with no gaps. Scaffold: A series of connected contigs with gaps of unidentified sequence ("N's") in between. N50: A statistical measure of average scaffold or contig size in a genome assembly. Specifically, 50% of the total assembled sequence is in scaffolds/contigs N50 or larger. Dovetail GenomicsTM, LLC ("Dovetail") is a private genomics company based in Santa Cruz, California. Dovetail specializes in the acquisition and analysis of long-range genomic information. Dovetail is the sole supplier of the ChicagoTM service for long-range proximity ligation and sequencing of genomic libraries. Dovetail is also the sole supplier of the HiRise scaffolding software pipeline. Dovetail has filed internationally for patent protection for these technologies. Additionally, Dovetail has obtained licenses, including exclusive licenses, for technologies related to its service. The following specialized services are required for the research mission of USDA, ARS, Stored Products Insect and Engineering Research Unit. The research will benefit from the extended scaffolding capabilities that Dovetail can provide, and give gene sequence data to use in downstream applications to develop new control technologies for stored product pests. Dovetail Genomics has been identified as the sole provider of the ChicagoTM service and is the only known vendor that can produce this type of specified service. Pursuant to the authority of 41 U.S.C. 253(c)(1) and FAR 6.302-1, Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements. The services will be provided for the USDA, ARS, CGAHR, Stored Products Insect and Engineering Research Unit in Manhattan, KS. The Government intends to award a firm fixed price purchase order on or about August 10, 2016. This Notice of Intent 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 4:00PM Central Standard Time, August 9, 2016. 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: USDA-ARS-WBSC Shalunda Mix 141 Experiment Station Road Stoneville, MS. 38776-0225 shalunda.mix@ars.usda.gov
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/notices/cef346712f2d35b700328290ce0369c5)
- Place of Performance
- Address: USDA, ARS, SPIERU, 1515 COLLEGE AVENUE, MANHATTAN, Kansas, 66502, United States
- Zip Code: 66502
- Zip Code: 66502
- Record
- SN04206046-W 20160804/160803000041-cef346712f2d35b700328290ce0369c5 (fbodaily.com)
- Source
-
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