127EAV26Q0125 Wheat Sequencing Responses to Questions 9.22.2026 Update.pdf

127EAV26Q0125 Wheat Sequencing

Responses to Questions

1. Will USDA ship the prepared library pools to the contractor’s lab, or must the contractor arrange pickup? If shipment is required, who is responsible for packaging and shipping costs?

USDA will ship the libraries to the contracted lab, and USDA is responsible for packaging and shipping costs.

2. Will all 22 pools be provided together or in batches? If they arrive in batches, does a separate 21-calendar-day delivery deadline begin upon receipt of each batch?

Pools will be sent in batches and will not be provided all at one time. The 21-calendar-day delivery deadline for each submitted batch begins upon receipt of that batch by the contractor.

3. If a USDA-prepared pool fails the required QC checks, should the contractor report the failure and await a replacement pool, or is additional preparation or remediation expected under the fixed price?

If a USDA prepared pool fails pre-sequencing QC, the contractor should report the failure to the designated USDA Technical Point of Contact for the contract. Appropriate remediation will be discussed with the contractor. If remediation is determined to be re-construction, re-submission, and re-QC of the pooled library, this will be performed by the USDA at the USDA’s expense. In instances where contractor QC checks are grossly inconsistent with internal USDA QC checks, the contractor may be requested to repeat a QC check at their own expense (e.g., where compelling evidence of a technical failure on the contractor’s part exists).

4. Could you please provide the specific library structure? Evaluating the construct details helps our sequencing team determine whether the libraries are balanced prior to confirming dedicated flow cell or lane allocations.

This answer serves to provide confirmation that USDA supplied libraries will be balanced, and that dedicated lane/flow cell allocation for USDA prepared libraries is a requirement for this award.

5. The solicitation specifies ten 1x150 Single-End High flow cells. In our standard daily laboratory workflow, single-end libraries are multiplexed and sequenced under paired-end conditions alongside routine runs. Please let us know if executing single-end libraries under paired-end sequencing conditions is acceptable to the end-user.

Multiplexing of USDA prepared libraries is not acceptable for this requirement. Lane/flow cell sharing of non-USDA prepared libraries with USDA prepared libraries is not acceptable for this requirement.

6. Standard output variation within ±5% on shared lanes falls within normal operational limits. Please note that multiplexing alongside complex third-party library types (such as 10x ATAC) can lower overall lane Q30 scores.

See answer above regarding lane/flow cell sharing with non-USDA prepared libraries for this requirement.

7. If dedicated flow cell sequencing is confirmed, we will provide all required FASTQ files, FastQC reports, and flow cell reports detailing pass-filter polony counts, Q-scores, and yield statistics.

See answer above confirming dedicated flow cell sequencing for USDA prepared libraries for this requirement.

8. What library kit was used to make the libraries and most importantly, what adapters were used?

USDA prepared libraries for this requirement are not constructed using a commercial kit. Adapters used in USDA prepared libraries are designed to be Illumina TruSeq-like.

9. Does the USDA have a system to upload to or am I expected to put the data onto a system and provide credentials to the end researchers?

The contractor is responsible for hosting sequencing deliverables (e.g., FASTQ files) on a secure site and for providing credentials to the designated USDA Point of Contact to access and download hosted deliverables. The USDA will not provide the contractor access to a system for this purpose.