Sample data for analysis of sequence variation in HIV
<p>These are downsampled interleaved paired fastq datasets from Jair et. 2019 (<a href="https://doi.org/10.1371/journal.pone.0214820">https://doi.org/10.1371/journal.pone.0214820</a>). The datasets were prepared by:</p> <ol> <li>Downloading original data from NCBI SRA (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517147)</li> <li>Trimming contaminating Nextera adapters using trim-galore</li> <li>Mapping reads against nxb2 reference of HIV genome (K03455.1) with BWA MEM</li> <li>Restricting mapped reads to <em>pol</em> gene vicinity (K03455.1:2000-5100)</li> <li>Downsampling mapped data to ~10% of the original with Picard's DownsampleSam</li> <li>Converting BAM to Interleaved Fastq with Picard's SamToFastq</li> <li>Gzipping resultant interleaved paired fastq files</li> </ol>
ShareScore
44/100
Overall dataset sharing score
Score breakdown
These five areas show where the dataset supports — or may limit — practical reuse.
- Stewardship
- 8
- Harmonization
- 8
- Access
- 16
- Reuse readiness
- 8
- Engagement
- 4