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run_all.sh
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run_all.sh
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#!/bin/bash
set -e -o pipefail
usage (){
echo " -1 <reads_1> short read pair 1 [ required ]"
echo " -2 <reads_2> short read pair 2 [ required ]"
echo " -l <long_reads> long reads file [ required ]"
echo " -d <draft> draft assembly [ default: none]"
echo " -o <output_prefix> prefix of the output files [ default: hypo]"
echo " -B <long_read_map> mapping of long reads to draft [ default: none]"
echo " -t <threads> the number of threads to use. [ default: 1 ]"
echo " -m <sortmem> the memory used to sort alignment files [ default: 1G ]"
echo " -@ <sortthreads> the threads used to sort alignment files [ default: 10 ]"
echo " -k <kmer length> the length of the solid kmer used [ default: 17 ]"
echo " -s <estimated_size> estimated genome size (suffix K/M/G accepted) [ default: 3G ]"
echo " -M <kmcmem> max memory to be used by KMC (in GB) [ default: 12 ]"
echo " -T <tempdir> directory to store intermediate files [ default: temp/ ]"
echo " -D debug mode [ default: disabled ]"
echo " -h display this help and exit"
exit 1
}
reads1=""
reads2=""
longreads=""
longbam=""
draft=""
threads="1"
sortmem="1G"
kmerlen="17"
tempdir="temp/"