#!/bin/bash

VARS="--breaklen 200 --mincluster 31 --diagdiff 5 --diagfactor 0.12 --maxgap 90 --minmatch 15"
INPUTS="--prefix out ../../data/S_lycopersicum_scaffolds.fa ../../data/S_lycopersicum_chromosomes.fa"
CMD="time ./nucmer --maxmatch --delta --extend --coords --optimize --nosimplify ${INPUTS}"
echo $CMD
$CMD
