simple-bowtie2-pe-to-ref

#!/bin/bash

ref=$1
reads1=$2
reads2=$3
output=$4

refbase=$(basename ${ref} .fasta)

bowtie2-build ${ref} ${refbase}

bowtie2 -p8 --fr --phred33 -x ${refbase} \
        -1 ${reads1} \
        -2 ${reads2} \
    | samtools view -bS - > ${output}.bam

samtools sort -O bam -T ${output} ${output}.bam > ${output}.sorted.bam

samtools index ${output}.sorted.bam