Questions_and_Answers_0626_0001.docx
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- Attached to
- DNA SEQUENCING Federal contract opportunity
- Solicitation number
- 140G0126Q0162
About this file
This is a Questions and Answers document for USGS Eastern Ecological Science Center's DNA sequencing solicitation (RFQ 140G0126Q0162). The document clarifies key technical requirements and preferences for PCR amplicon sequencing services over a one-year base period with four-year option periods.
The government will provide indexed libraries ready for sequencing rather than extracted eDNA, with quality control verification performed by the sequencing core. The preferred sequencing platform is Illumina-based technology, specifically the NextSeq 1000 with 600 cycle cartridges, as the previously specified NovaSeq 6000 has been discontinued. The government declined consideration of non-US sequencing alternatives, such as Macrogen Korea, and prefers to avoid newer platforms like Element Biosciences AVITI despite potentially equivalent performance metrics. Required output specifications include approximately 1 million paired-end reads per sample at specific markers or amplicons, with typical throughput of 384 samples per NextSeq P2 600 cycle cartridge run, targeting quality scores of at least 75% Q30 with 2x250 read configuration. The government will not accept alternative library preparation chemistries, as they have made significant investments in UDI indices, primers, and Pippin Preps equipment and require consistency with their established preparation methodology since 2022. Analysis results must be delivered within 60 days of sample receipt to the EESC facility in Laurel, Maryland. Quotation responses are due by June 30, 2026, at 2:00 p.m. Mountain Time, with an anticipated award date of July 10, 2026. This is a Total Small Business Set Aside under NAICS code 541380 (Testing Laboratories and Services) with a $19 million size standard, and offerors must be registered in SAM at the time of award.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| Sol_140G0126Q0162_Amd_0001.pdf | ||
| Sol_140G0126Q0162.pdf | ||
| B08__Instructions_To_Offerors_Attachment_1.docx | DOCX document | |
| Attachment_2_Schedule_of_Services.xlsx | XLSX spreadsheet |
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Questions and Answers
1. Will we provide extracted eDNA as starting material?
No, we will provide a pool of indexed libraries ready for sequencing after the sequencing core does any needed QC they require (verification of concentration, etc).
2. NovaSeq 6000 is retired from our lab and not available anymore. Alternatively, we can support NextSeq 1000 (600 cycle). Would you be interested in using NextSeq instead?
We may be interested in running the NextSeq 1000 600 cycle cartridge.
3. If you are okay with ship samples out of the country, you can use NovaSeq 6000 by our parent company in Korea, Macrogen Korea. Please let me know if this option works for you. (i dont think this will be a doable option) I agree, would prefer not to ship samples out of the country for sequencing when there are providers in the US.
4. Do you have output amount you need for each samples?
This is project dependent. We generally get sufficient depth from 384 samples run on one NextSeq P2 600 cycle xleap cartridge.
5. What is the coverage (eg 0.0x) required for each sample? Or how much GB/sample are desired?
This is hard to nail down. I'd say approximately 1 million paired end reads per sample at a specific marker/amplicon is a good target.
6. Is the researcher open to other technology platforms (eg Element Biosciences AVITI platform) as long as the system offers the same or better quality scores of >=75% Q30 and is still 2x250 reads? The NovaSeq 6000 has generally been discontinued and replaced with the NovaSeq X Plus. So many offers may not be able to offer services on NS6000 anyway.
We would prefer to stick with Illumina, since all of our samples to date have been done with Illumina chemistry and we feel we can be fairly confident Illumina will be supported for a long time into the future, whereas newer companies like Aviti are still being adopted.
7. Researcher open to non-Illumina NGS library prep chemistries assuming UDI's are used?
We prefer to make our own libraries and control the amplification, size selection, and indexing strategies. Therefore, we are only interested at this time in providing ready made libraries we have made to sequencing core labs. We have significant investment in UDI indices, primers, Pippin Preps, etc. We also want to maintain consistency in preparation method across libraries that have been prepared following this general approach since 2022.
File details come from the government source that posted it. Updated .