Description of files in the directory "GenotypingPipeline"

genotypingPipeline.sh   Commands used to prepare the RAD loci and
                        genotype the individuals from the raw read files
                        (available from :
                        http://www.ncbi.nlm.nih.gov/bioproject/750675)
                        The instructions to run the pipeline are in the
                        comments within the file

cat2fa.py               Python script used by genotypingPipeline.sh to 
                        prepare the fasta files of the RAD loci. Tested
                        with Python 2.7, NOT compatible with Python 3

checkSeg.py             Python script used by genotypingPipeline.sh to 
                        check the segragation of the RAD loci. Tested
                        with Python 2.7, NOT compatible with Python 3
