SOW_PacBio_v2_1.doc
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- Attached to
- PacBio Revio sequencing Federal contract opportunity
- Solicitation number
- 140G0325Q0104
About this file
This Performance Work Statement (PWS) details a project by the US Geological Survey to sequence the genome of the rough-skinned newt (Taricha granulosa) using PacBio Revio technology. The work involves four key phases: library preparation and quality checks, sequencing across 12 Revio flow cells, potential ISOSEQ library preparation, and data transfer to the Principal Investigator. Performance requirements include producing sequence data with an N50 > 15,000 nucleotides and > 100 GB of data per flow cell, with raw data to be uploaded to the NCBI database by February 2027.
The sources sought announcement seeks qualified businesses in the Testing Laboratory sector (NAICS 541380) to perform the sequencing work. The project has a three-month performance period beginning after award, with all work to be completed at the vendor's facility. The government is conducting market research to determine contractor availability and will accept electronic capability statements until May 5, 2025, at 3:00 PM PST. No costs will be reimbursed for response preparation, and this is not a formal solicitation but a market research initiative to inform the acquisition strategy.
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PERFORMANCE-BASED WORK STATEMENT
I. GENERAL INFORMATION
A. Introduction.
The overall goal of the work is to produce PacBio Revio sequence data for the genome of the rough-skinned newt, Taricha granulosa.
B. Background.
Amphibians are among the last of the vertebrates to enter the whole-genome sequencing phase due to the large size and high percentage of repetitive sequence content in their genomes (Liedtke et al., 2018; Womack et al., 2022). However, decreasing sequencing costs and advances in assembly methods have permitted researchers to invest in new reference genomes for a small but growing set of amphibian species. For example, the genomes of Rana draytonii and Hyliola regilla are currently being assembled as part of the California Conservation Genomics Project. Nevertheless, challenges to building amphibian genome resources remain. Despite California being a hotspot for salamander diversity, salamanders were completely excluded from CCGP efforts because their genomes are very large (>30 GB) and thus expensive to build. The proposed work would help produce the data that are necessary to build a reference genome for the rough-skinned newt, Taricha granulosa. Reference genomes are necessary for modern conservation programs and critical for any state-of-the-art research program (Matthews and Vosshall, 2020).
C. Definitions/Applicable Documents.
Reference genome: an assembly of all DNA from a single individual of a species into a set of sequences that span each chromosome. The format is usually fasta or GenBank.
PacBio Revio: a sequencing technology that can produce very long reads of DNA, upwards of 30,000 bp
D. Scope.
The scope of the work is the preparation and sequencing of libraries of high molecular weight DNA from T. granulosa on PacBio Revio flow cells, along with any necessary troubleshooting to increase yield.
II. WORK REQUIREMENTS
A.
Technical Requirements.
1. Describe specific work requirements and/or work products.
Phase 1: Library preparation and quality checks Phase 2: Sequencing across 12 Revio cells Phase 3: Potential ISOSEQ library prep and sequencing
Phase 4: data transfer to PI Tarvin
2. Criteria for acceptance of Product or Service (how will contractor's compliance be measured).
The sequence quantity and quality B.
Deliverables.
1. Characteristics for work product described in II.A.1., identified by name and quantity.
The sequence data should have an N50 > 15,000 nt and > 100 GB of data produced per flow cell
2. Delivery dates for work/product to be completed and point of delivery.
Three months after the date of award
III.
SUPPORTING INFORMATION
A. Place of Performance.
Vendor’s facility B. Period of Performance.
Three months C. Government Furnished Property (GFP):
N/A D.
Special Considerations.
1. Key personnel qualifications Experience sequencing a variety of difficult genomes on the PacBio Revio technology
2. Data Rights, Safety, Environment.
Data will be transferred to Tarvin when complete for genome assembly. Raw data will be uploaded to the NCBI database and made publicly available by February 2027.
3. Security/Privacy issues.
N/A
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