Additional Questions and Answers.docx
DOCX document 19 KB Posted
- Attached to
- Metagenomic or Shotgun Sequencing
- Solicitation number
- 1232SA26Q0300
About this file
This file is a Questions and Answers document addressing vendor inquiries regarding RFQ 1232SA26Q0300 for metagenomic or shotgun sequencing services. The document clarifies technical and logistical requirements for the USDA Agricultural Research Service procurement.
Key clarifications include: control sequencing requires one set of positive and negative (water) controls per batch totaling two controls; vendors should use their existing positive control standards and provide information about them; DNA samples will be shipped to vendors in 96-well plate format by the USDA at government expense; vendors must include return shipping costs in their quotes; pricing should be submitted as a total contract price rather than per-sample unit pricing; the first shipment contains 177 samples and the second contains 133 samples, each in separate packages; the required data output is 3-5 million read pairs using a 2x150 base pair configuration, equating to 0.9 to 1.5 gigabases of data; and while the Illumina sequencing platform is mandatory, library preparation kits from compatible vendors such as NEB or Roche are acceptable if compatible with Illumina instruments, with vendor proposals to be evaluated based on the preparation method details provided. Vendors must complete sequencing and data transfer within 45 days of sample receipt.
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Other files
| File | Type | Posted |
|---|---|---|
| RFQ 1232SA26Q0300 - MOD 1.pdf | ||
| SCA Wage Rates.pdf | ||
| RFQ 1232SA26Q0300.pdf |
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Additional Questions and Answers
1. Do we need to sequence the controls on every flow cell or lane or is one sufficient for each batch?
Yes, the controls will be sequenced. One set of controls for each batch will be sufficient.
2. Do you have specific controls in mind, i.e. for the positive controls using a bacterium with comparable to expected %GC content? If so, could I please know a little more information on the species of the bacteria targeted?
Usually someone running the sequencing has a positive control already selected that they use for all their work. It is usually a mixture of DNA from known origins. Whatever positive control the sequencers already have in place will suffice, but they should give us the information. We can add ‘information on the positive control used should be made available by the company.’
3. Could you clarify how many controls total will be required?
The total controls they will need to sequence will be 2. One positive and one water only.
4. Does this mean that you require the cost of the sample shipment to the offeror to be included in the quote? Or are the statements in the RFQ only in reference to shipping the remaining DNA back to the USDA?
Shipping samples to the offerer will be paid for by the USDA. Shipping the remaining DNA back to the USDA by the offerer will be paid for by the offerer and must be included in the quote.
5. For the Pricing element of the Submission Requirements, does the "Unit price" refer to the cost of 1 of the 310 total samples?
The offerer can provide the total price for everything in the contract. The price of sequencing can depend on the number of samples and preparation. Therefore, we don’t need a per sample price just the total price for everything that is included.
6. Are the initial 177 samples expected to ship in one package containing all 177 samples?
Yes
7. Are the subsequent 133 samples expected to ship in one package containing all 133 samples?
Yes
8. The required data volume is listed as 3 to 5 million read pairs. This is a slightly different, but meaningful, language convention than we typically see. Can you please clarify whether you intend:
· 3-5 million read pairs E.g. if 2x150bp read configuration used, this equates to .9 to 1.5 Gbp of data
· 3-5 million paired reads E.g. If 2x150bp read configuration used, this equates to 0.45 to 0.75 Gbp of data
We expect a 2x150 bp read configuration read pairs, which based on the question above equates to 0.9 to 1.5Gbp of data
9. In what format will the DNA samples be provided?
· For example, will the DNA be transported in 1.5ml snap-cap centrifuge tubes, or in 96-well plates (preferred)?
The samples will be shipped in a 96 well plate format
10. We understand that the USDA wants to use the Illumina sequencing platform to match previous sequencing data. However, the scope is not specific regarding library preparation. Is an Illumina branded Library Prep kit required, or is an alternate name brand (i.e. NEB, Roche) also acceptable?
The offerer should provide details on which preparation method they will be used. Although the Illumina instrument is selected, the library prep does not necessarily have to be illumina as long as they are compatible. This will be evaluated as part of the quote.
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