Test data for RonaQC - mapped SARS-CoV-2 reads

<p>This dataset includes test data for <a href="https://ronaqc.netlify.app/">RonaQC</a></p> <p>RonaQC accepts mapped SARS-CoV-2 reads (BAM format), generated from the SARS-CoV-2 bioinformatic pipelines like ARTIC, and any control samples from the respective sequencing run (negative/positive) as input. It will then assess the levels of cross contamination and primer contamination in the samples, and determine if the samples are reliable for detecting SARS-CoV-2, phylogenetic analysis, and/or submission to public databases.</p> <p><br> The dataset includes SARS-CoV-2 sequenced reads compiled by <a href="https://github.com/CDCgov/datasets-sars-cov-2">CDCgov/datasets-sars-cov-2</a>&nbsp;[1].&nbsp;</p> <p>These were reads were processed using the <a href="https://github.com/connor-lab/ncov2019-artic-nf">ncov2019-artic-nf pipelines</a>, which is a Nextflow pipeline for running the <a href="https://github.com/artic-network/fieldbioinformatics">ARTIC network&#39;s fieldbioinformatics tools</a>,&nbsp;with a focus on ncov2019.&nbsp;</p> <p><br> This dataset includes:&nbsp;</p> <ul> <li><strong>FailedQC </strong>- A cohort of 24 samples failed basic QC metrics, covering 8 possible failure scenarios, Illumina platform, amplicon-based approach&nbsp;&nbsp; &nbsp;</li> <li><strong>VOCRepresentatives </strong>- A cohort of 16 samples from 10 representative CDC defined VOI/VOC lineages as of 06/15/2021, Illumina platform, amplicon-based approach&nbsp;&nbsp; &nbsp;</li> <li><strong>Test </strong>- Smaller test samples, including sequenced negative controls of varying quality</li> </ul> <p>[1] &nbsp;Timme, Ruth E., et al. &quot;Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.&quot; PeerJ 5 (2017): e3893.&nbsp;</p>