PWS for solicitation.pdf

Performance Work Statement (PWS) Project: Sequencing Service

GENERAL INFORMATION

1.0 Background and Purpose: The Barley and Oat Improvement project, part of the USDA-ARS

Small Grains and Potato Germplasm Research Unit at Aberdeen, Idaho, investigates the genetic control of oat characteristics that contribute to agronomic performance and marketability. These investigations contribute towards developing efficient breeding strategies for crop improvement.

Oat lines have been sampled from the USDA National Small Grains Collection to represent the genetic diversity present in domesticated oat. High density sequence-based molecular markers are needed to characterize genomic variation among individual oat lines so that genomic regions influencing oat traits may be identified..

2.0 Definitions: QC – Quality Control; Gb – Gigabase; POC – Point of Contact; PE –

Paired End; DNA - Deoxyribonucleic acid; ddRAD – Double digest restriction site associated DNA

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

DNA sample QC – Analysis of DNA from 800 Avena sativa samples for quality/quantity suitability for library prep.

ddRAD-Seq library prep and QC – Preparation of a ddRAD sequencing library using the PstI-MspI restriction enzyme combination. 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 2G raw data per sample.

Bioinformatic analysis – SNP genotype calling. Report submitted via email with delivery of data via online access.

4.0 Deliverable / Schedule:

o DNA will be submitted to the contractors on an as-needed basis via delivery service throughout the performance period.

o Every submitted DNA 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 All reports will be delivered via email to the government POC.

o All final sequencing data (raw and SNP calls) 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 SNP calls To receive data for analysis No later than thirty

(30) business days after confirmation of raw sequencing data

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:

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.

6.0 Travel: N/A