directory_list.txt

TEMPLATE_DIR="/opt/CONCOMPRA/scripts" #adjust to script directory - for installation from git, will generaly be in the form of "/home/user/CONCOMPRA/scripts"
PRIMER_SET="/data/primer_set.fa" #adjust to the directory where the primer file
#primer file should be a fasta file in which:
#The head primer should have "head" in its name (case-insensitive).Likewise for the tail primer.
#Both sequences should be those that appear in the cDNA's sense strand.
# sequences are not limited to the primers itself but can also include anchor sequences; longer sequences generaly give better results

MIN=1400 #minimal sequence length to retain (min filter)
MAX=1700 #maximal sequence length to retain (max filter)
MERGE_CONSENSUS=1 #similarity on which to cluster consensus sequences across samples [0,1]
READS_CONSENSUS=40 #the number of reads to subsample from a cluster to draft the consensus sequence
THREADS=8 # set number of threads to use