Shell script for running the digital normalization part of khmer

diginorm.sh

#!/bin/sh

#script to run digital normalization
#####
#files
R1=$1 #"R1_001" forward fastq reads
R2=$2 #"R2_001" reversed fastq reads
COM=$3 #"combined_001" interleaved reads

#paths
KHMER_SCRIPTS="~/khmer/scripts" #path to khmer/scripts
SICKLE="/mnt/EXT/Schloss-data/kiverson/sickle-master/"

#parameters
K=20
C=20
X_PRAM='1e10'

#####
python $KHMER_SCRIPTS/interleave-reads.py $R1 $R2 -o $COM.fq
$SICKLE/sickle pe -c $COM.fq -M $COM.trimmed.fq -t sanger
python $KHMER_SCRIPTS/normalize-by-median.py -k $K -C $C -x $X_PRAM --savetable $COM.trimmed.kh -p $COM.trimmed.fq
python $KHMER_SCRIPTS/filter-abund.py -V $COM.trimmed.kh $COM.trimmed.fq.keep
rm $COM.trimmed.kh

#second round of normalization to remove high abundance k-mers