Generic 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. The reference genome can be provided as a GenBank file.

Generic variant calling

A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs:

• A genbank file with the reference genomes
• A collection of paired fastqsanger files

The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the Reporting workflow.

Workflow can be accessed ...