Workflows

Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq

This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.