Questions and Answers 2.pdf
PDF 71 KB Posted
- Attached to
- Shotgun Metagenomic Sequencing
- Solicitation number
- 12505B23Q0248
About this file
This document contains questions and answers regarding a federal contract for shotgun metagenomic sequencing. The contract requires 250 bp paired-end sequencing with a minimum of 50,000 reads per sample, however the questions clarify that 2x150 bp reads with 6 GB of data per sample is acceptable. While de novo transcriptome generation was listed, RNAseq is not included in the deliverables. The bioinformatics analysis must be completed within 35 business days of receiving all 200 Drosophila suzukii samples for sequencing. The related federal contract opportunity is solicitation number 12505B23Q0248 for shotgun metagenomic sequencing from the US Department of Agriculture Agricultural Research Service.
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Other files
| File | Type | Posted |
|---|---|---|
| Provisions and Clauses Full and Open.pdf | ||
| Questions and Answers.pdf | ||
| Updated Statement of Work.pdf | ||
| Statement of Work.pdf | ||
| Wage Determination.pdf | ||
| Provisions and Clauses.pdf |
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Text version
Q’s: Under 3.0 – Technical Requirement
Metagenomic sequencing:
The scope states “250 bp paired-end sequencing, with a minimum of 0.05M reads per sample”.
• While 2 x 250 bp sequencing is available, that is not typically required for shotgun sequencing
(vs. PE 2 x 150 bp standard). Please confirm that PE 2 x 250 BP is the requirement.
• 0.05M (50K) reads per sample: The bioinformatics required cannot be met with only 50K reads per sample. The bioinformatics specified require at least 500K reads minimum per sample, and we recommend 10M reads per sample to provide high-quality de novo assembly for downstream metagenomic analysis. Please confirm that 0.05M reads per sample is correct.
Under bioinformatics services:
The first statement states “Conduct de novo transcriptome generation”. This cannot be provided without adding a full RNAseq workflow to the scope of supply. Please confirm if RNAseq for each sample should or should not be included in the deliverables.
Timeline of delivery of the bioinformatics package: The scope requires the pangenome to be assembled from all 200 D. suzukii samples. That means all 200 samples must first be received and sequenced before the bioinformatics can be completed. Please confirm that delivery of bioinformatics at 35 business days from completion of sequencing of sample #200 is acceptable.
A’s: It should be 2X150 bp reads.
6 GB per sample.
No transcriptomics.
35 days turn around is perfect.
File details come from the government source that posted it. Updated .