SOLICITATION NOTICE
B -- Next-Generation DNA and RNA Sequencing Services
- Notice Date
- 5/3/2022 8:51:29 AM
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 541714
— Research and Development in Biotechnology (except Nanobiotechnology)
- Contracting Office
- USDA ARS MWA AAO ACQ/PER PROP PEORIA IL 61604 USA
- ZIP Code
- 61604
- Solicitation Number
- 12505B22Q0088
- Response Due
- 5/16/2022 3:00:00 PM
- Archive Date
- 05/31/2022
- Point of Contact
- Aaron Dimeo
- E-Mail Address
-
aaron.dimeo@usda.gov
(aaron.dimeo@usda.gov)
- Small Business Set-Aside
- SBA Total Small Business Set-Aside (FAR 19.5)
- Description
- This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will NOT be issued. Solicitation number 12505B22Q0088 is issued as a request for quote (RFQ). The solicitation document and incorporated FAR provisions and clauses are those in effect through Federal Acquisition Circular 2022-06. This solicitation will be a 100% Total Small Business Set-Aside. The associated NAICS code is 541714, Research and Development in Biotechnology (except Nanobiotechnology), with a small business size standard of 1,000 employees and the PSC code is B529. The Department of Agriculture (ARS) has the need for the following services: 001) Next-Generation DNA and RNA Sequencing Services Scope of Work: The USDA-ARS Biological Control of Insects Research Laboratory in Columbia, Missouri is requesting quotes for next-generation DNA and RNA sequencing services. To conduct DNA and RNA sample sequencing using next-generation technologies. To generate de novo genomic and transcriptomic assemblies of clean nucleic acid sequencing data. To conduct metagenomic amplicon sequencing. To conduct bioinformatic analyses of nucleic acid sequencing data. The services provided under this service agreement are to be valid for one calendar year with an option to extend through a second year. Background: The objective is the completion of Next-Generation nucleic acid sequencing and bioinformatic analyses that further and enhance current research at the USDA-ARS, Biological Control of Insects Research Laboratory in Columbia, Missouri. These services will accelerate progress on Objectives 1-4 of the in-house project 5070-22000-038-00-D. Technical Requirements & Specifications: Genomic sequencing: Conduct �genome survey� sequencing using the NovaSeq platform. 150 bp paired-end sequencing, with a minimum of 24 Gb of raw data per sample. Specifications: Service provider to provide sample QC analysis; library preparation; statistical analyses of data production and quality; de novo genomic assembly; bioinformatic analyses of genomic assembly including, but not limited to, K-mer analysis, GC content, repeat content rate evaluation, heterozygous rate evaluation, genome size evaluation, contamination inspection. The service provider is expected to complete genomic sequencing services as described above for a minimum of 1 and a maximum of 5 samples during year one and in option year two, if elected. Transcriptomic sequencing: Conduct �mRNA-seq� sequencing using the NovaSeq platform. 150 bp paired-end sequencing, with a minimum of 24 Gb of raw data per sample Specifications: Service provider to provide sample QC analysis; library preparation; statistical analyses of data production and quality; de novo transcriptomic assembly; bioinformatic analyses of transcriptomic assembly including, but not limited to, gene functional annotation using at least seven databases, GO/COG/KEGG classification, CDS prediction, SNP/INDEL calling, SSR analysis, gene expression analysis within and between sample groups, correlation analysis (as applicable), differential expression analysis (as applicable), enrichment analysis, protein interaction analysis. The service provider is expected to complete transcriptomic sequencing services as described above for a minimum of 1 and a maximum of 60 samples during year one and in option year two, if elected. Metagenomic sequencing: Conduct �amplicon metagenomic� sequencing using the NovaSeq platform. 250 bp paired-end sequencing, with a minimum of 0.05 M reads per sample. Specifications: Service provider to provide sample QC analysis; PCR amplification; amplicon library preparation; bioinformatic analyses of amplicon sequencing, including but not limited to, data split and reads merging, data quality control, filtration and chimera removal, taxonomic analysis, alpha diversity analysis, beta diversity analysis, functional prediction. The service provider is expected to complete metagenomic sequencing services as described above for a minimum of 1 and a maximum of 80 samples during year one and in option year two, if elected. Bioinformatic services: Conduct de novo transcriptome generation and bioinformatic analyses using previously generated raw nucleic acid sequencing data. Specifications: Service provider to provide statistical analyses of data production and quality; data quality control, filtering reads to remove adapters and low quality reads; de novo transcriptomic assembly; bioinformatic analyses of transcriptomic assembly including, but not limited to, gene functional annotation using at least seven databases, GO/COG/KEGG classification, CDS prediction, SNP/INDEL calling, SSR analysis, gene expression analysis within and between sample groups, correlation analysis (as applicable), differential expression analysis (as applicable), enrichment analysis, protein interaction analysis. The service provider is expected to complete bioinformatic sequencing services as described above for a minimum of 1 and a maximum of 60 samples during year one and in option year two, if elected. Government Furnished: Nucleic acid samples or raw sequence data. Key Deliverables: For all sequencing services (genomic, transcriptomic and metagenomic) described above, service provider is expected to: Provide client with sample QC analysis and await client approval prior to commencement of sample sequencing. Provide client with all raw sequencing data in the form of .fastq files, assemblies in the form of .fasta files, and bioinformatic analysis data in tabulated (e.g., Excel) format. For Bioinformatic (only) services described above, service provider is expected to: Provide client with assemblies in the form of .fasta files, and bioinformatic analysis data in tabulated (e.g., Excel) format. For all services: Provide client with access to a web portal through which project forms and reports can be completed and project progress can be monitored. Delivery: Deliver of all data and results is to be made through a secure, service provider-based File Transfer Protocol server directly to client named on individual project estimate within 35 business days of sample QC approval for sequencing projects, or within 20 business days for bioinformatic analysis projects. The Government anticipates award of one Indefinite Delivery, Indefinite Quantity (IDIQ) award. Evaluation Factors: The basis for award will be Lowest Price, Technically acceptable.�The Government intends to make a single Indefinite Delivery, Indefinite Quantity (IDIQ) contract award based on the lowest price technically acceptable (LPTA) quote. ""LPTA"" means the best value is expected to result from selection of the technically acceptable quote with the lowest evaluated price.�Pursuant to FAR 52.212-2, the criteria for evaluation are: (1) Price; (2) Technical Requirements. The lowest priced quote will be evaluated first; if NOT found acceptable, the next lowest priced quote will be evaluated, and so on until a technically acceptable quote is identified. The government will NOT review higher priced quotes if the lowest priced quote is determined to be technically acceptable. For quoted services to be considered technically acceptable, they must meet ALL of the technical requirements identified in this solicitation. Submitting a Quote: Offerors responding to this announcement shall submit their quote in accordance with FAR 52.212-1. The applicable FAR clauses and provisions that apply to this acquisition are included with the attached quote submission form (SF1449). The Government anticipates award of a single Indefinite Delivery, Indefinite Quantity (IDIQ) contract. To be eligible for an award, all contractors must be registered in the System for Award Management (SAM) with a current and active registration at the time of their quote submission. A contractor can contact SAM by calling 1-866-606-8220 or e-mail at www.sam.gov. NO EXCEPTIONS. A Unique Entity Identifier (UEI) number is required in order to register.�Vendor MUST include their UEI# on their quote. The submission and payment of invoices for orders placed against the resulting single IDIQ contract will be made through the Invoice Processing Platform (IPP). As such, contractors must be currently registered or register in IPP in order to be able to submit and receive payment on invoices for orders placed against the resulting contract award. Offerors responding to this announcement shall submit their quote on�SF1449�(see attachments), provide a written Quality Assurance Plan in response to the Quality Assurance Surveillance Plan provided in the attachments to the SF1449 (between the Statement of Work and the Wage Rate Determination), and provide completed FAR clauses and provisions. The quote should include all fees, delivery charges, and/or surcharges. This will be a tax-exempt purchase. Failure to demonstrate compliance will constitute sufficient cause to reject a quote without further discussions. All responsible sources may submit a quote which will be put into considered for award. Questions in regards to this combined synopsis/solicitation must be submitted through email (NO calls with questions will be accepted) and are due by NO later than�5:00 PM CT on Tuesday, May 10, 2022. Answers to any questions received by that time will be�posted as an amendment to this combined synopsis/solicitation. NO questions will be answered after this date unless determined to be in the best interest of the Government. Only electronic submissions made via email will be accepted (NO phone calls OR quotes submitted by USPS mail will be accepted). Please email all quotes in writing on the SF1449 with a written QAP and completed FAR clauses and provisions to��aaron.dimeo@usda.gov by NO later than�Monday, May 16, 2022 at 5:00 PM Central Time (CT). Note: Be absolutely certain to reference the RFQ number �12505B22Q0088� and/or title of the solicitation �Next-Generation DNA and RNA Sequencing Services� in the subject, body, and/or attachments of your quote submission email to ensure your submission can be located and attributed to this solicitation. Failure to do so could potentially result in your submission being deemed �unresponsive� and as a result your quote may NOT be put into consideration for award (as your quote may NOT be located when searching the recipients emails to ensure ALL responses to the solicitation have been logged before making an award determination).
- Web Link
-
SAM.gov Permalink
(https://sam.gov/opp/913043bb07e04d23a4cd9abaac4a17de/view)
- Place of Performance
- Address: Columbia, MO 65203, USA
- Zip Code: 65203
- Country: USA
- Zip Code: 65203
- Record
- SN06315088-F 20220505/220503230102 (samdaily.us)
- Source
-
SAM.gov Link to This Notice
(may not be valid after Archive Date)
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