ronaQC
Source code for web resource, 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 software is live on https://ronaqc.netlify.app/
Deploy
npm run build
netlify deploy --prod
Test data
There are two datasets to demonstrate/test ronaQC:
A very simple dataset (30MB)
Test data is available here: https://ronaqc.netlify.app/ronaqc_small_test.zip
This includes:
- mapped reads of three sequenced controls of varying quality
- mapped reads of two genuine SARSCOV2 samples.
A more exhaustive dataset (1GB)
Test data is available here: https://zenodo.org/record/7018405
This includes:
- SARS-CoV-2 sequenced reads from major VOCs.
- SARS-CoV-2 sequenced reads from samples that are known to have failed (for different reasons).
- The test data from above, with one additional sample.
VOC and failed QC data are taken from CDCgov/datasets-sars-cov-2.