diff --git a/genomix/genomix-driver/compare.sh b/genomix/genomix-driver/compare.sh
new file mode 100755
index 0000000..c2b4e53
--- /dev/null
+++ b/genomix/genomix-driver/compare.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+
+#set -x
+
+if [ $# -ne 2 ]; then
+	echo "Please provide 2 parameters: infile.readids, outdir"
+	echo "For example:	$0 /data/users/anbangx/testdata/tail600000 /data/users/anbangx/graphbuild"
+	exit 1
+fi
+
+INFILE=$1
+OUTDIR=$2
+
+rm -rf $OUTDIR
+mkdir -p $OUTDIR
+
+$CMD="/data/users/anbangx/hyracks/genomix/genomix-driver/target/appassembler/bin/genomix"
+#run original dataset by hyracks
+/data/users/anbangx/hyracks/genomix/genomix-driver/target/appassembler/bin/genomix -kmerLength 55 -localInput $INFILE -localOutput $OUTDIR/original-hyracks -pipelineOrder BUILD_HYRACKS 2>&1 | tee $OUTDIR/original-hyracks/log
+
+#run original dataset by hadoop
+/data/users/anbangx/hyracks/genomix/genomix-driver/target/appassembler/bin/genomix -kmerLength 55 -localInput $INFILE -localOutput $OUTDIR/original-hadoop -pipelineOrder BUILD_HADOOP 2>&1 | tee $OUTDIR/original-hadoop/log
+
+#random the data 
+#sort -R $INFILE | head 600000 > $INFILE+"_random"
+
+#$#RANDOMINPUT 
+#run original dataset by hyracks
+/data/users/anbangx/hyracks/genomix/genomix-driver/target/appassembler/bin/genomix -kmerLength 55 -localInput ${INFILE}_random -localOutput $OUTDIR/random-hyracks -pipelineOrder BUILD_HYRACKS 2>&1 | tee $OUTDIR/random-hyracks/log
+
+#run original dataset by hadoop
+/data/users/anbangx/hyracks/genomix/genomix-driver/target/appassembler/bin/genomix -kmerLength 55 -localInput ${INFILE}_random -localOutput $OUTDIR/random-hadoop -pipelineOrder BUILD_HADOOP 2>&1 | tee $OUTDIR/random-hadoop/log
+
+#sort the output and diff
+sort -n $OUTDIR/original-hyracks/data >  $OUTDIR/original-hyracks/sort
+sort -n $OUTDIR/original-hadoop/data >  $OUTDIR/original-hadoop/sort
+sort -n $OUTDIR/random-hyracks/data >  $OUTDIR/random-hyracks/sort
+sort -n $OUTDIR/random-hadoop/data >  $OUTDIR/random-hadoop/sort
+
+diff $OUTDIR/original-hyracks/sort $OUTDIR/random-hyracks/sort > ~/diff/original-random_hyracks
+diff $OUTDIR/original-hadoop/sort $OUTDIR/random-hadoop/sort > ~/diff/original-random_hadoop
+diff $OUTDIR/original-hyracks/sort $OUTDIR/original-hadoop/sort > ~/diff/hyracks-hadoop_original
+diff $OUTDIR/random-hyracks/sort $OUTDIR/random-hadoop/sort > ~/diff/hyracks-hadoop_random
+
+