SOURCES SOUGHT
Q -- Sequencing and Analysis of Turf genomes
- Notice Date
- 5/13/2020 1:20:02 PM
- Notice Type
- Sources Sought
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- USDA ARS PWA AAO ACQ/PER PROP ALBANY CA 94710 USA
- ZIP Code
- 94710
- Solicitation Number
- 12905B20Q05132020
- Response Due
- 5/19/2020 1:00:00 PM
- Archive Date
- 06/03/2020
- Point of Contact
- Jeffery A. Ridenour, Phone: 309-363-5914
- E-Mail Address
-
jeffery.ridenour@usda.gov
(jeffery.ridenour@usda.gov)
- Description
- The USDA, Agricultural Research Service (ARS) is conducting market research to support Forage and Range Research Center for Sequencing and Analysis of Turf genomes for the�Construction of�one proximity ligation library per 3 gigabases of the organism�s genome, using the provided tissue, blood, or cell culture sample. This is a Sources Sought notice. This is NOT a solicitation for quotations. The purpose of this notice is to obtain information.� North American Industry Classification System (NAICS) code for the proposed acquisition, 541990. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. The government is seeking capability statements from businesses capable of meeting the below minimum specification requirements: Scope of Work: Proximity Ligation Library Preparation: Construct one proximity ligation library per 3 gigabases of the organism�s genome, using the provided tissue, blood, or cell culture sample. Vendor will sequence ~20M PE75bp reads and map the data back to the draft assembly to assess library quality. Libraries to be sequenced on an Illumina HiSeq X instrument and aim to sequence ~100M read pairs per Gbp of the organism's genome size (30X sequence coverage). Assembly Informatics Package: Vendor will scaffold the draft assembly (minimum N50 of 100kb is required) through HiRise software pipeline using the proximity ligation data. If applicable and depending upon the metrics and complexity of the genome and HiRise output, Vendor will perform a TAD analysis on the genome, generated from Vendor proximity ligation libraries. The following are the input constraints for TAD analysis: � 40% of read pairs should map at a distance > 1Kbp � Genome size 40% of genome uniquely mappable � Coverage: 100 M read pairs per 1Gb Deliverables: Deliver the results files to Customer electronically via secure FTP. The Results shall consist of: HiRise Assembly deliverables include: � The HiRise assembly in FASTA format � A report summarizing key assembly statistics, features of the proximity ligation library, and a linkage density plot of the proximity ligation library data � 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 file(s) containing alignments of the proximity ligation library read pairs mapped to the draft assembly � TAD Analysis deliverables, if applicable, include: � TAD calls at 10kbp, 25kbp, and 50kbp � CTCF binding sites � A/B compartmental organization � Isochore locations � Guide to loading and viewing data in HiGlass � Summary report Target Timeline/Milestones: The total run time for this project will be approximately 10 weeks from the receipt of draft assembly, sample, and raw read data when required. Respondents shall furnish sufficient technical information necessary for the Government to conclusively determine that they are capable of meeting the technical requirements identified above. Firms believing they can meet the requirements are encouraged to respond electronically with no less than the following information: � Business name, DUNS number, business address, business website, business size status (i.e., SB, VOSB, SDVOSB, HUBZone SB, SDB, WOSB, LB), point of contact name, mailing address (if different from business address), phone number, and email address; � Sufficient descriptive literature that unequivocally demonstrates that offered equipment will meet or exceed above specifications; � Descriptive material necessary for the government to determine whether the service offered meets the technical requirements; � Interested Parties must respond with capability statements by email to jeffery.ridenour@usda.gov on or before May 19, 2020 at 3:00 PM Central Standard Time. Personal visits for the purpose of discussing this requirement are strongly discouraged and will NOT be scheduled. THIS IS NOT A REQUEST FOR QUOTE. Disclaimer and Important Notes: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization�s qualifications to perform the work. The government is not responsible for locating or securing any information, not identified in the response. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in beta.SAM.gov. However, responses to this notice will not be considered adequate responses to a solicitation. Point of Contact Mr. Jeffery Ridenour, Contract Specialist, 2413 Nashville Road, Bowling Green, KY. 42101; Phone 309-363-5914; Email: jeffery.ridenour@usda.gov. Place of Performance USDA ARS FRRC 700 N 1100 E Utah State University Logan, UT. 84322
- Web Link
-
SAM.gov Permalink
(https://beta.sam.gov/opp/2a206004160a47309e4a72d5458a9b36/view)
- Place of Performance
- Address: Logan, UT 84322, USA
- Zip Code: 84322
- Country: USA
- Zip Code: 84322
- Record
- SN05656786-F 20200515/200513230159 (samdaily.us)
- Source
-
SAM.gov Link to This Notice
(may not be valid after Archive Date)
| FSG Index | This Issue's Index | Today's SAM Daily Index Page |