Simple trimming/mapping/variant calling pipeline for uncomplicated viral genomes
This is run via snakemake with rules trim, map, pile-up, etc
The repo is currently adapted to an Enterovirus D68 project with Richard Neher, Robert Dyrdak, Emma Hodcroft, and Jan Albert, and has been used in Dyrdak et al. 2019 and Hodcroft et al. 2020.