COVID-19 sequence analysis on Illumina Amplicon PE data

sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE

This workflow implements an iVar based analysis similar to the one in ncov2019-artic-nf , covid-19-signal and the Thiagen Titan workflow . These workflows (written in Nextflow, Snakemake and WDL) are widely in use in COG UK , CanCOGeN and some US state public health laboratories.

This workflow is also the subject of a Galaxy Training Network tutorial (currently a Work in Progress ). It differs from this workflow in that it does not use lofreq and is aimed at rapid analysis of majority variants and lineage/clade assignment with pangolin and nextclade .

TODO:

1. Add support for QC using negative and positive controls
2. Integrate with phylogeny tools including IQTree and UShER (and possibly more).