HAVoC can be run to analyze FASTQ files within a directory by typing the following in terminal:
sh HaVoC.sh [FASTQ directory]
The target directory must contain matching FASTQ files for forward (R1) and reverse (R2) reads, which can be either gzipped (*.fastq.gz) or uncompressed (*.fastq).
HAVoC needs to be in the same directory as NexteraPE-PE.fa and ref.fa.
The following options can be manually changed in the script file depending on your preferences: