Q_A_0001.pdf
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- Attached to
- NEWT GENOME AND ANNOTATION Federal contract opportunity
- Solicitation number
- 140G0325Q0126
About this file
This document is a Questions and Answers (Q&A) file for a federal contract opportunity involving newt genome sequencing and annotation. The Q&A provides technical clarification about the genomic data to be provided to the vendor, including >20 TB of sequence data from three platforms (Oxford Nanopore, Illumina HiC, and PacBio) generated from a single newt individual. Key technical details include specific read depths for each sequencing platform: Oxford Nanopore at 15X, Illumina HiC at 30X, and PacBio at 30X. The data was pre-sequenced, with multiple sample preparations to ensure a diverse sequence representation, and will be used to assemble the newt genome. The responses also clarify that "two independent sources" refers to genome assembly quality assessment software like QUAST, merqury, BUSCO, or GenomeQC, and confirm that a 30X HiC assay was generated for haplotyping purposes.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| Sol_140G0325Q0126_Amd_0001.pdf | ||
| Sol_140G0325Q0126.pdf | ||
| Combined_Synopsis_Solicitation_Attachments.pdf |
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140G0325Q0126amd01 Page 3 of 3
1. What form of sample will be provided, i.e. extracted and purified Newt DNA, or frozen tissue, or FFPE?
A: >20 TB of sequence data from Oxford Nanopore, Illumina (HiC), and PacBio will be provided to the vendor.
2. The SOW states that “a single individual” will be provided. Is that correct? Or will a cohort of samples be provided as a baseline to assemble the newt genome?
A: The data that will be given to the vendor was generated for a single individual.
This makes assembly easier because only two haplotypes are present in the dataset.
3. Is there a requirement to run the sample(s) in duplicate or triplicate, or is running a single sequencing assay per platform acceptable for each assay?
A: Sequencing will be performed prior to providing the vendor with the sequencing data. Each sample was prepared multiple times to ensure a diverse set of sequences representing the genome is included in the resulting data.
4. Please define “two independent sources” criteria (Work Requirements A2). Does a single run (of a single individual) on a PacBio platform, an Oxford Nanopore platform and an Illumina short read platform for WGS meet the Scope?
A: The sources refer to software that can assess the quality of a genome assembly, such as QUAST, merqury, BUSCO, or GenomeQC.
5. What is the required read depth for the sequencing assays?
A: Oxford Nanopore: 15X; HiC (sequenced on Illumina platform): 30X; PacBio: 30X
6. In addition to an Illumina short read WGS assay, is a Hi-C assay (for haplotyping) required for this project? “Haplotype phased” implies the need for a Hi-C assay or similar. Or is a different assay required?
A: Yes, we generated 30X HiC data on the Illumina platform.
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