Attachment_A_-_Questions_and_Answers-140G0225Q0111_0001.pdf
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- Attached to
- DNA SEQUENCING SERVICES
- Solicitation number
- 140G0225Q0111
About this file
This document is a Questions and Answers (Q&A) attachment for Request for Quote (RFQ) 140G0225Q0111 issued by the United States Geological Survey (USGS) Great Lakes Science Center. The RFQ seeks high throughput, short read sequencing services specifically on the Illumina NovaSeq X platform to generate whole genome data for native salmonids in the Great Lakes. The sequencing service includes quality control analysis and delivery of demultiplexed sequence data from genomic DNA libraries prepared by the USGS Molecular Ecology Lab.
The Q&A document clarifies three key points: (1) the Illumina platform is mandatory to prevent platform-based batch effects, (2) the requirement involves 2 master premade libraries, each needing 4 lanes of PE150 sequencing with a 25B flow cell, which can be pooled across one entire flow cell (8 lanes), and (3) the specific library preparation kit to be used is the SRSLY NGS Library Prep Kit for Illumina NanoPlus Uracil+. The dual-index combinations for the 89 individuals in the 2 pre-made libraries are unique, allowing for consolidated sequencing.
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| Sol_140G0225Q0111_Amd_0001.pdf | ||
| Sol_140G0225Q0111.pdf |
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Attachment A
Questions and Answers
RFQ 140G0225Q0111
The United States Geological Survey (USGS) Great Lakes Science Center has a requirement for high throughput, short read sequencing services on the Illumina platform to generate whole genome data for native salmonids in the Great Lakes. This service includes quality control analysis, sequencing on the Illumina NovaSeq X platform, and delivery of demultiplexed sequence data from genomic DNA libraries prepared by the
USGS-Great Lake Science Center's Molecular Ecology Lab.
1. Question #1:
“The service description ins mentioning sequencing on the IlluminaNovaSeq X platform.
Is it also possible to provide the sequencing service using other sequencing (non
Illumina) platforms that provide equal of better sequencing data output and quality? Or is the Illumina/NovaSeq platform mandatory?”
USGS’s Responses: The Illumina platform is mandatory. The data generated will be combined with previously generated Illumina short read sequence data on the NovaSeq X platform. A different sequencing platform could introduce platform-based batch effects and negatively impact data analysis.
2. Question #2:
“Is the requirement 4 lanes per pre-made library or spread the 2 pre-made libraries across
8 lanes?”
USGS’s Responses: Each of the 2 master premade libraries needs the equivalent of 4 lanes of PE150 sequencing with a 25B flow cell on the
Illumina NovaSeq X platform. The dual-index combinations for the 89 individuals contained in these 2 pre-made libraries are unique, therefore the
2 libraries could be pooled evenly to be run across one entire 25B flow cell (8 lanes).
3. Question #3:
“Which library preparation kit will you use for the NovaSeq X Plus sequencing?”
USGS’s Responses: The prep kit used for these libraries is the SRSLY NGS
Library Prep Kit for Illumina NanoPlus Uracil+.
Attachment A
Questions and Answers
RFQ 140G0225Q0111
The United States Geological Survey (USGS) Great Lakes Science Center has a requirement for high throughput, short read sequencing services on the Illumina platform to generate whole genome data for native salmonids in the Great Lakes. This service includes quality control analysis, sequencing on the Illumina NovaSeq X platform, and delivery of demultiplexed sequence data from genomic DNA libraries prepared by the
USGS-Great Lake Science Center's Molecular Ecology Lab.
File details come from the government source that posted it. Updated .