runCorr.sh

#!/bin/bash

# Author: Ehsan Haghshenas (ehaghshe[at]sfu[dot]ca)

if [ "$#" -lt 5 ]; then
   echo "USAGE: ./runCorr.sh pacbio.fasta illumina.fastq outDirectory outPrefix threads"
   exit
fi

EXEDIR=$(dirname "${BASH_SOURCE[0]}")
CURRDIR=`pwd`
LRFILE=$(readlink -e "${1}")
SRFILE=$(readlink -e "${2}")
OUTDIR=$(readlink -f "${3}")
OUTPRE=$(basename "${4}")
NTHREAD=$5
BWAOPTIONS="-aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5 -t $NTHREAD"

BWA=${EXEDIR}/bin/bwa-proovread
SAM=${EXEDIR}/bin/samtools
SPALG=${EXEDIR}/bin/spCorrection
OEAALG=${EXEDIR}/bin/oeaCorrection

UNCORR=${OUTDIR}/${OUTPRE}_uncorr
CORR=${OUTDIR}/${OUTPRE}_sp
ITER1=${OUTDIR}/${OUTPRE}_iter1
ITER2=${OUTDIR}/${OUTPRE}_iter2

mkdir -p ${OUTDIR}
# rm -f ${OUTDIR}/*
ln -s -f ${LRFILE} ${UNCORR}.fasta

${BWA} index ${UNCORR}.fasta
${BWA} mem ${BWAOPTIONS} ${UNCORR}.fasta ${SRFILE} > ${ITER1}.sam
rm ${UNCORR}.fasta.amb ${UNCORR}.fasta.ann ${UNCORR}.fasta.bwt ${UNCORR}.fasta.pac ${UNCORR}.fasta.sa
${SAM} view -bS ${ITER1}.sam | ${SAM} sort -@ ${NTHREAD} - | ${SAM} view -h -o ${ITER1}.sort.sam -
rm ${ITER1}.sam
${SPALG} -l ${UNCORR}.fasta -a ${ITER1}.sort.sam -t ${NTHREAD} > ${ITER1}.fasta
rm ${ITER1}.sort.sam

${BWA} index ${ITER1}.fasta
${BWA} mem ${BWAOPTIONS} ${ITER1}.fasta ${SRFILE} > ${ITER2}.sam
rm ${ITER1}.fasta.amb ${ITER1}.fasta.ann ${ITER1}.fasta.bwt ${ITER1}.fasta.pac ${ITER1}.fasta.sa
${SAM} view -bS ${ITER2}.sam | ${SAM} sort -@ ${NTHREAD} - | ${SAM} view -h -o ${ITER2}.sort.sam -
rm ${ITER2}.sam
${SPALG} -l ${ITER1}.fasta -a ${ITER2}.sort.sam -t ${NTHREAD} > ${CORR}.fasta
rm ${ITER2}.sort.sam