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- #!/bin/bash
- #
- # Author: Jue Ruan
- #
- REF=$1
- CTG=$2
- # change this path to your mummer
- MUM=/public/software/mummer-323-intel
- if [ -z $REF ] || [ -z $CTG ]; then
- echo "Usage: $0 <ref> <ctg>"
- exit
- fi
- echo "REF:$REF"
- echo "CTG:$REF"
- $MUM/nucmer --mumreference -l 100 -c 1000 -d 10 --banded -D 5 $REF $CTG
- $MUM/delta-filter -i 95 -o 95 out.delta > out.best.delta
- $MUM/dnadiff -d out.best.delta
- $MUM/mummerplot out.best.delta --fat -f -png
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