#!/bin/bash

READDIR="/home/reads/" # Directory all reads are stored in
GENOME="/home/ref_chr_17.novo" # reference genome 


for file in $READDIR*.1.fastq; do prefix=${file#$READDIR}; prefix=${prefix%%.1.fastq}; novoalign -d $GENOME -f $READDIR$prefix.1.fastq $READDIR$prefix.2.fastq -o SAM > $prefix.sam; done

