viral-ngs: genomic analysis pipelines for viral sequencing

Contents

Description of the methods

This is a base module that provides basic utility functions, some short read aligners, and samtools and Picard.

Command line tools

reports.py - produce various metrics and reports

illumina.py - for raw Illumina outputs

broad_utils.py - for data generated at the Broad Institute

file_utils.py - utilities to perform various file manipulations