diff --git a/tests/script_tests/run_comparison_to_ground_truth.sh b/tests/script_tests/run_comparison_to_ground_truth.sh
new file mode 100755
index 0000000..6ed2a47
--- /dev/null
+++ b/tests/script_tests/run_comparison_to_ground_truth.sh
@@ -0,0 +1,73 @@
+#!/bin/bash
+
+# This is to compare the results of CMash against a brute force calculated containment indicies.
+# WARNING: this uses a LOT of memory and is CPU intensive as well, so use with caution (and use on a server)
+
+# In case you have multiple versions installed (eg. Metalign as well as CMash), make sure python is looking in the right place:
+export PYTHONPATH="$(dirname $(dirname "`pwd`"))":$PYTHONPATH
+
+#Make sure the correct CMash is being pulled from
+testFile=$(python -c "from CMash import MinHash as MH; print(MH.__file__)")
+parentDir=`dirname $PWD`
+parentDir=`dirname ${parentDir}`
+correctFile="${parentDir}/CMash/MinHash.py"
+if [ "$testFile" == "$correctFile" ];
+then
+  echo "Files are correct"
+else
+  echo "Files are not correct"
+  exit 1
+fi
+
+testOrganism="../Organisms/taxid_1192839_4_genomic.fna.gz"
+maxK=5
+kSizes="4-${maxK}-1"
+numHashes=10
+containmentThresh=.01
+locationOfThresh=-1
+
+scriptsDir="${parentDir}/scripts"
+modulesDir="${parentDir}/CMash"
+
+# make the training database
+echo "Training on data"
+rm TrainingDatabase.h5 2> /dev/null
+rm TrainingDatabase.tst 2> /dev/null
+/usr/bin/time python ${scriptsDir}/MakeStreamingDNADatabase.py filenames.txt TrainingDatabase.h5 -n ${numHashes} -k ${maxK}
+if test -f TrainingDatabase.h5; then
+  if test -f TrainingDatabase.tst; then
+    echo "Training file successfully created"
+  else
+    echo "SOMETHING WENT WRONG!!!!"
+    exit 1
+  fi
+  else
+    echo "SOMETHING WENT WRONG!!!!"
+    exit 1
+fi
+
+echo "Classifying sample with CMash"
+outName="est_results.csv"
+rm ${outName} 2> /dev/null
+# make a streaming pre-filter
+/usr/bin/time python ${scriptsDir}/StreamingQueryDNADatabase.py ${testOrganism} TrainingDatabase.h5 ${outName} $kSizes --sensitive -l $locationOfThresh -c $containmentThresh
+if test -f ${outName}; then
+  echo "sensitive classify successful"
+  cat ${outName}
+else
+  echo "SOMETHING WENT WRONG!!!!"
+  exit 1
+fi
+
+echo "Computing ground truth containment indicies"
+outName="true_results.csv"
+rm ${outName} 2> /dev/null
+# make a streaming pre-filter
+/usr/bin/time python ${modulesDir}/GroundTruth.py ${testOrganism} TrainingDatabase.h5 ${outName} $kSizes -l $locationOfThresh -c $containmentThresh
+if test -f ${outName}; then
+  echo "sensitive classify successful"
+  cat ${outName}
+else
+  echo "SOMETHING WENT WRONG!!!!"
+  exit 1
+fi