The goal of COVID-19-Biohackathon 2020 (COVID-19-BH20) is to develop and gather computational tools that can be useful for studying the biology of the virus and the disease.
The COVID-19 Programme in Workflow Hub aims to gather workflows for the analysis of COVID-19 molecular biology data and their metadata. In this programme, all workflows and their metadata will be curated and made interoperable, reusable and reproducible. All workflows and their metadata will be easily accessible to everyone
The workflow for Illumina-sequenced ampliconic 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 amplicon primer sequences off reads with the ivar
package. In addition, this workflow uses ivar also to identify amplicons
affected by primer-binding site mutations and, if possible, excludes reads
derived from such