Sequencing Services for Soybean Samples
Closed Pre-Solicitation Posted
This opportunity was awarded. See the award notice from , or the latest solicitation from .
- Solicitation number
- 1116725-SS
- Agency
- Northeast Area Field Research Implementation and Information Delivery, Department of Agriculture
- Responses due
- Set-aside
- No set-aside
Opportunity facts
- NAICS code
- 541990 All Other Professional, Scientific, and Technical Services
- Place of performance
- Beltsville, Maryland 20705, United States
Notice details come from SAM.gov. Updated .
About this opportunity
The United States Department of Agriculture Agricultural Research Service seeks sequencing services for 440 soybean samples to support genetic research. The contractor must provide whole genome sequencing of at least 20x coverage and variant calling for each sample, with a minimum data output of 20 gigabytes per sample and 85% or higher quality scores. Responses must demonstrate the ability to complete the work within 60 working days of sample receipt and quality control. Responses to the sources sought notice are due by January 19, 2023.
No set-aside is designated for this requirement. Interested parties should identify if they are a large or small business under NAICS code 541990 and provide contact information in their response. The sequencing data will enable analysis of genes related to crop traits such as disease resistance, yield, and nutrition to support the goals of the agency's Action Plan.
Notice text
2 versions
Update #2 · Latest ·
Sources Sought Notice -Soybean Sequencing
Sources Sought #1116725-SS
This is a Sources Sought notice Only. This is NOT a solicitation for proposals, proposal abstracts, or quotations. This Sources Sought is issued for information and planning purposes only as part of USDA ARS market research and does not itself constitute an RFQ.
Background
Soybean and common bean are among the most important crops in the U.S., with an annual value of $34 and $2 billion, respectively. These crops are important sources of protein for animal feed or human food. Soybean is also an important source of oil and a top U.S. export commodity. To cope with biotic and abiotic stress that cause >20% yield loss and demands for enhanced quality, breeders need to discover genes from new resources and develop approaches to accelerate the breeding processes. Molecular genotyping and sequencing of populations and individuals is critical to determine the novelty and positions of genes in the genome and assist selection. This research and goals are relevant to the NP301 Action Plan, Component 1. Crop Genetic Improvement; Problem Statement 1A: Trait discovery, analysis, and superior breeding methods.
Requirements
Sequencing of our 440 soybean samples must have a minimum of 20 Gb of data for each sample, which is about 20x coverage of the WGS, SNP + InDel + SV calls among all samples, i.e by aligning the WGS of each sample to the reference genome individually, then combine all the aligned file to call variants, guarantee library preparation, and data quality (Q30 for ≥ 85%) for each sample that passes QC. These sequences will allow us to detect genes or other genetic factors that control resistance to disease and insects, productivity and the nutritional quality of soybean. Work must be done within 60 working days after receiving and QC of samples.
*we are interested in SNP + InDel + SV+ CNV calls among all samples, i.e by aligning the WGS of each sample to the reference genome individually, then combine all the aligned file to call all these variants. In addition, we also need the annotation of the variants (such as SNPs and Indels) based on the GFF3 file.
- genome strain to which the alignment should be performed 1: Wm82.a2.v1
- cultivar / strain for the alignment to be used 2: Willams82
Work must be done within 60 working days after receiving and QC of samples. The vendor shall delivery the assays electronically as a compressed file in “.tar” format.
The Contractor Shall:
This Sources Sought is only for the purpose of identifying potential sources as part of USDA ARS market research. The Government does not intend to make an award based on responses to this inquiry. This notice does not constitute a commitment by the Government.
Responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible.
The purpose of this notice is to obtain information regarding the availability and capability of qualified sources including any Small Businesses; HUBZone small business; service-disabled, veteran-owned small business; 8(a) small business; veteran-owned small business; woman-owned small business; or small disadvantaged businesses. Please state if you are a large business or a small business according to the NAICS code listed in this Sources Sought.
All information submitted in response to this announcement is voluntary, and the Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the Government.
Any organization responding to this notice should ensure that its response defines how it can specifically meet the specifications for the items requested. 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 review of the responses received, a Combined Synopsis solicitation notice may be published on Sam.gov.
Submit the Following:
- Capability Statement that demonstrates your ability to meet the specific requirements, including Company Contact Info
- SAM.gov UEI Number
- Identify if you are a large business or a small business with NACIS 541990.
Original Point of Contact: All responses to this Sources Sought Notice must be received by January 19, 2024, by 9:00 AM PDT, the specified due date and time to be considered.
Email responses to Elizabeth Wilson at Elizabeth.Wilson2@usda.gov.
Responses will not be returned. Responders are solely responsible for all expenses associated with responding to this Inquiry.
Do not submit pricing information in response to this Request.
Update #1 ·
Sources Sought Notice -Soybean Sequencing
Sources Sought #1116725-SS
This is a Sources Sought notice Only. This is NOT a solicitation for proposals, proposal abstracts, or quotations. This Sources Sought is issued for information and planning purposes only as part of USDA ARS market research and does not itself constitute an RFQ.
Background
Soybean and common bean are among the most important crops in the U.S., with an annual value of $34 and $2 billion, respectively. These crops are important sources of protein for animal feed or human food. Soybean is also an important source of oil and a top U.S. export commodity. To cope with biotic and abiotic stress that cause >20% yield loss and demands for enhanced quality, breeders need to discover genes from new resources and develop approaches to accelerate the breeding processes. Molecular genotyping and sequencing of populations and individuals is critical to determine the novelty and positions of genes in the genome and assist selection. This research and goals are relevant to the NP301 Action Plan, Component 1. Crop Genetic Improvement; Problem Statement 1A: Trait discovery, analysis, and superior breeding methods.
Requirements
Sequencing of our 440 soybean samples must have a minimum of 20 Gb of data for each sample, which is about 20x coverage of the WGS, SNP + InDel + SV calls among all samples, i.e by aligning the WGS of each sample to the reference genome individually, then combine all the aligned file to call variants, guarantee library preparation, and data quality (Q30 for ≥ 85%) for each sample that passes QC. These sequences will allow us to detect genes or other genetic factors that control resistance to disease and insects, productivity and the nutritional quality of soybean. Work must be done within 60 working days after receiving and QC of samples.
Work must be done within 60 working days after receiving and QC of samples. The vendor shall delivery the assays electronically as a compressed file in “.tar” format.
The Contractor Shall:
This Sources Sought is only for the purpose of identifying potential sources as part of USDA ARS market research. The Government does not intend to make an award based on responses to this inquiry. This notice does not constitute a commitment by the Government.
Responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible.
The purpose of this notice is to obtain information regarding the availability and capability of qualified sources including any Small Businesses; HUBZone small business; service-disabled, veteran-owned small business; 8(a) small business; veteran-owned small business; woman-owned small business; or small disadvantaged businesses. Please state if you are a large business or a small business according to the NAICS code listed in this Sources Sought.
All information submitted in response to this announcement is voluntary, and the Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the Government.
Any organization responding to this notice should ensure that its response defines how it can specifically meet the specifications for the items requested. 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 review of the responses received, a Combined Synopsis solicitation notice may be published on Sam.gov.
Submit the Following:
- Capability Statement that demonstrates your ability to meet the specific requirements, including Company Contact Info
- SAM.gov UEI Number
- Identify if you are a large business or a small business with NACIS 541990.
Original Point of Contact: All responses to this Sources Sought Notice must be received by January 19, 2024, by 9:00 AM PDT, the specified due date and time to be considered.
Email responses to Elizabeth Wilson at Elizabeth.Wilson2@usda.gov.
Responses will not be returned. Responders are solely responsible for all expenses associated with responding to this Inquiry.
Do not submit pricing information in response to this Request.
Attachments
| File | Type | Posted |
|---|---|---|
| STATEMENT OF WORK.docx | DOCX document |
Notice history
| Notice | Type | Posted |
|---|---|---|
| Sequencing Services for Soybean Samples | Award Notice | |
| Sequencing Services for Soybean Samples | Solicitation | |
| Sequencing Services for Soybean Samples | Pre-Solicitation |
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