/ronaQC

Quality control of SARSCOV2 genomic data using mapped reads (bam)

Primary LanguageJavaScriptGNU General Public License v3.0GPL-3.0

ronaQC

Netlify Status

Node.js CI

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)

DOI 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.