This folder contains a Bourne shell script pipeline for preprocessing of HBS-seq data. It is not intended to be a 100% robust pipeline, but instead provides a reasonable starting point for local customisations. It has been tested only on a CentOS Linux system, but should work with few if any changes in other environments (e.g. MacOSX).
Start by editing fold.settings, and PLEASE read the scripts before
running them. In particular, fastq naming conventions may not match your data,
and paths to programs such as GATK likely need to be changed.