PWS.pdf
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- Attached to
- Sequencing Service Federal contract opportunity
- Solicitation number
- 12805B21Q0437
About this file
This performance work statement outlines sequencing services required by the Agricultural Research Service Plains Area Field Research Implementation and Information Delivery office. The contractor will perform quality control checks, library preparation, and sequencing runs for various sample types including small RNA, messenger RNA, whole genome, and bisulfite whole genome sequencing. Key deliverables include quality control reports within three days of sample receipt, library preparation initiated within five days, sequencing run statistics within seven days, and data transfer within ten days. The contractor must have experienced laboratory staff and Illumina sequencing capabilities. Performance standards require meeting sequencing yield and quality thresholds with price reductions applied for shortfalls.
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Performance Work Statement (PWS) Project: Sequencing Service
GENERAL INFORMATION
1.0 Background and Purpose: The Fargo Small Grains Genotyping Lab investigates the genomics of small grains in the US. Our focus is to assist the community by providing genotyping service and performing primary research on the identification of gene regions that influence traits. Once found, this knowledge is used to accelerate breeding of better cultivars with high yield, excellent quality, and innate disease resistance. To do this high-throughput sequencing capacity is necessary to evaluate the genomes of populations to find these regions.
2.0 Definitions: QC – Quality Control; Gb – Gigabase; POC – Point of Contact; PE –
Paired End; DNA - Deoxyribonucleic acid; RNA - Ribonucleic acid
CONTRACTOR REQUIREMENTS
3.0 Technical Requirements/Tasks: {State each objective, task, or activity. Identify expected or desired outcome(s). Include provisions for the contractor to comply with all relevant quality standards. Identify any specific skill requirements needed to successfully complete the work} Premade Library QC – Analysis of quality and concentration of submitted sequencing library with electrophoresis method. Quality report submitted via email.
sRNA-seq: Small RNA sequencing library generation – Preparation of sequencing library from submitted total RNA. Quality report submitted via email mRNA-seq: Messenger RNA sequencing library generation – Preparation of sequencing library from submitted total RNA. Quality report submitted via email WGS: Whole Genome Sequencing- Illumina library generation – Preparation of sequencing library from submitted DNA. Quality report submitted via email bWGS: Bisulfite Whole Genome Sequencing -Illumina sequencing library generation – Preparation of sequencing library from submitted DNA. Quality report submitted via email
NovaSeq S4 150PE Full lane Sequencing –Loading of library, reporting run statistics, and delivery of data via online access. Require > 650 Gb of sequencing data/lane
NovaSeq 150PE Partial lane Sequencing - Loading of library, reporting run statistics, and delivery of data via online access. Customer will request a specific amount (in Gb) of sequencing data.
HiSeq 150PE Full lane Sequencing – Loading of library, reporting run statistics, and delivery of data via online access. Require > 100 Gb of sequencing data/lane
1 GB 150PE Sequencing Service – Loading of library, reporting run statistics, and delivery of data via online access. Require ≥ 1 Gb of sequencing data. (1GB is equivalent to 3.33 million 150PE reads
4.0 Deliverable / Schedule:
o Sequencing libraries and DNA/RNA will be submitted to the contractors on an as-needed basis via delivery service throughout the performance period.
o Every submitted DNA/RNA sample will be QC analyzed and converted into sequencing libraries and sequenced to the customers specifications as described in the contractor’s submission documentation.
o Every submitted library will be QC analyzed and pooled for sequencing to the customers specifications as described in the contractor’s submission documentation.
o All reports will be delivered via email to the government POC.
o All final sequencing data (raw and assembled) will be provided via a download link.
o Timely submission of deliverables is essential to successful completing this requirement.
Schedules for deliverables are specified in below.
Key Deliverables Item No.
Deliverable
Objective
Due
1 QC report of submitted sample
To identify if sample should be re-submitted
No later than three
(3) business days after submitted sample is received
2 Library Prep & Sequencing
To perform the task Initiated no later than five (5) business days after confirmation of sample QC
3 Sequencer Run Statistic Report
To identify if the sequencing run was successful
No later than seven
(7) business days after confirmation of sample QC
4 Sequencing Data To receive data for analysis No later than ten
(10) business days after confirmation of library quality
5.0 Government Furnished: N/A
6.0 Travel: N/A
7.0 Contractor’s Key Personnel: Contractor must have laboratory staff experienced in assaying the quality of sequencing libraries and running the Illumina instruments.
8.0 Security Requirements: Data submission portal will be password protected.
9.0 Data Rights: The data will be solely owned by the government and the contractor will have no rights or obligations to the data once it is transferred.
10.0 Section 508 – Electronic and Information Technology Standards: N/A
11.0 Performance Requirement Measures: {Indicate how the government will measure the contractor's performance for specific tasks or work critical to the mission essential items).
o Payment deduction is generally a remedy for non-performance, not as an incentive. Non- Monetary incentives may include award term contract arrangement (contractor is awarded periods of performance) or Past Performance for quality level of performance.
Performance Objective
Required Task or Deliverable
Performance Standard
Method of Surveillance
Positive/Negative Incentive % for NOT meeting the Task
Desired Outcome or what must be accomplished as the end result of this contract.
Stare the task or deliverable that must be accomplished for the desired result.
State error rates, accuracy rates, completion of milestones, cost control, etc. The government must set the standards.
(State the method and who performs the surveillance
Incentives can be monetary, non-monetary, realist, attainable and built on performance objectives and standards. Use positive or negative incentives when performance exceeds standard or is below standards.
Sequencing Library Preparation
Sequencing Library (sRNA, mRNA, WGS, bWGS)
Sufficient quality and quantity to meet the requested sequencing amounts
Inspection of run statistic report and assessment once data is received
1% of service price every 1% decrease from requested sequencing amount -1% of lane price every 1% decrease from 80% Q30 of the requested sequencing amount.
Illumina
Service
NovaSeq S4 150PE Service – Full Lane
Greater than 650 Gb of sequencing data with >80% Q30
Inspection of run statistic report and assessment once data is received
-1% of lane price every 1% decrease from 650 Gb sequencing data -1% of lane price every 1% decrease from 80% Q30
Service
HiSeq 150PE Service – Full Lane
Greater than 90 Gb of sequencing data with with >80% Q30
Inspection of run statistic report and assessment
-1% of lane price every 1% decrease from 100 Gb sequencing data
Service
NovaSeq 150PE Service – Partial Lane
Greater than the amount of sequencing data ( in Gb) with >80% Q30
Inspection of run statistic report and assessment
-1% of lane price every 1% decrease from every Gb sequencing data requested
Service
1 GB 150 Service Greater than 1 Gb of sequencing data with with >80% Q30
Inspection of run statistic report and assessment
-1% of lane price every 1% decrease from 1 Gb sequencing data
Attachment: N/A
6.0 Travel: N/A
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