Shell script for data filtering:

#!/bin/bash

echo 'Finding fastqs in '$1
echo 'Using '$2' CPUs and '${3}'G mem'

base=`basename $1`
outdir=${base}_bbduk
mkdir $outdir

zcat ${1}/*_1.fastq.gz > $outdir/${base}_1.raw.fq
zcat ${1}/*_2.fastq.gz > $outdir/${base}_2.raw.fq

pigz -p $2 $outdir/${base}_*.raw.fq

echo ''
ls -al $outdir/${base}_1.raw.fq.gz
ls -al $outdir/${base}_2.raw.fq.gz
echo ''

bbduk.sh \
-Xmx${3}g \
threads=$2 \
in1=$outdir/${base}_1.raw.fq.gz \
in2=$outdir/${base}_2.raw.fq.gz \
out1=$outdir/${base}_1.bbduk.fq.gz \
out2=$outdir/${base}_2.bbduk.fq.gz \
ref=~/anaconda3/envs/main_env/opt/bbmap-38.22-0/resources/adapters.fa \
ktrim=r k=23 mink=11 hdist=2 maq=10 minlen=100 tpe tbo stats=${outdir}/bbduk.contaminants &> ${outdir}/bbduk.stats

echo ''
kmercountexact.sh -Xmx${3}g threads=8 in1=$outdir/${base}_1.raw.fq.gz in2=$outdir/${base}_2.raw.fq.gz khist=$outdir/${base}.raw.khist

echo ''
kmercountexact.sh -Xmx${3}g threads=8 in1=$outdir/${base}_1.bbduk.fq.gz in2=$outdir/${base}_2.bbduk.fq.gz khist=$outdir/${base}.bbduk.khist

echo ''
perl -lane 'if(/#/){next}else{print join(" ",$F[0],$F[1])}' $outdir/${base}.raw.khist > $outdir/${base}.raw.khist_jf.hist
perl -lane 'if(/#/){next}else{print join(" ",$F[0],$F[1])}' $outdir/${base}.bbduk.khist > $outdir/${base}.bbduk.khist_jf.hist