Major changes include:
- Adds an option for a pipeline that keeps a smaller, less comprehensive set of output files
- kmerFind.py: locates reads with a specific barcode, allowing for mismatches. Barcoded reads can either be trimmed or masked with N
- BARCODE: is the pipeline module wraper for kmerFind.py
- TRIM: added poly-base trimming, allowing for removal of long strings of
the same base from either end of the read and parallelized trimming - BLASTQC: allow for short reads (shorter than 50bp)
- launcher.sh: allow for running pre-configured pipeline instances in parallel using a csv config file
- run_bcl2fastq.sh: run Illumina bcl2fastq v2.17