Space: General
SEEK ID: https://dev.workflowhub.eu/projects/14
Public web page: Not specified
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Team created: 11th Dec 2020
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COVID-19: variation analysis reporting
This workflow takes table of variants produced by any of the other four variant calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates a list of variants by Samples and by Variant.
COVID-19: variation analysis on WGS SE data
This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.
COVID-19: variation analysis on WGS PE data
This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.
COVID-19: variation analysis on ARTIC PE data
The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and, if possible, excludes reads derived from such ...