Bioinformatics of ISD sequencing test

mkdir -p /gscratch/grandol1/AlfTnIsdCheck/rawreads

cd /gscratch/grandol1/AlfTnIsdCheck/rawreads

unpigz --to-stdout /project/gtl/data/raw/AlfTnIsdCheck/rawreads/ALF-TN-16S-COL2_S1_L001_R1_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - AlfCheck_R1_ ;
unpigz --to-stdout /project/gtl/data/raw/AlfTnIsdCheck/rawreads/ALF-TN-16S-COL2_S1_L001_R2_001.fastq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - AlfCheck_R2_

/project/gtl/data/raw/AlfTnIsdCheck/rawreads/run_parse_count_onSplitInput.pl

cd /project/gtl/data/raw/AlfTnIsdCheck/rawdata/

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh