Download reads from the SRA

download_sra_reads

#!/bin/bash

if [[ $# -ne 3 ]]; then
    >&2 echo "usage: download_sra_reads <acc_list.txt> <outdir> <num_threads>"
    exit 1
fi

NUM_THREADS="${3}"
OUTDIR="${2}"
ACC_LIST="${1}"

parallel --jobs ${NUM_THREADS} --retries 3 \
	 fastq-dump \
	 --defline-seq "'@\$ac \$sn/\$ri'" \
	 --defline-qual "'+\$ac \$sn/\$ri'" \
	 --split-e \
	 --disable-multithreading \
	 --outdir ${OUTDIR} \
	 {} \
	 <${ACC_LIST}