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

This dataset includes test data for RonaQC

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.

The dataset includes SARS-CoV-2 sequenced reads compiled by CDCgov/datasets-sars-cov-2 [1]. 

These were reads were processed using the ncov2019-artic-nf pipelines, which is a Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools, with a focus on ncov2019. 

This dataset includes: 

• FailedQC - A cohort of 24 samples failed basic QC metrics, covering 8 possible failure scenarios, Illumina platform, amplicon-based approach    
• VOCRepresentatives - A cohort of 16 samples from 10 representative CDC defined VOI/VOC lineages as of 06/15/2021, Illumina platform, amplicon-based approach    
• Test - Smaller test samples, including sequenced negative controls of varying quality

[1]  Timme, Ruth E., et al. "Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance." PeerJ 5 (2017): e3893.