diff --git a/non-regression-tests/run_nrt.sh b/non-regression-tests/run_nrt.sh
deleted file mode 100755
index e1c477d11f1a3367341ccb1f908a4d8605de0a90..0000000000000000000000000000000000000000
--- a/non-regression-tests/run_nrt.sh
+++ /dev/null
@@ -1,97 +0,0 @@
-#/bin/bash
-DATA_PATH=./data
-REF_RES_PATH=./reference_results
-
-## VL: decided to write the checking of results in python scripts rather than shel script for portability.
-
-
-echo "running non regression tests with default options"
-./run_HK97.sh || exit 1
-./run_lamda.sh || exit 1
-./run_P1.sh ||exit 1
-./run_N1.sh ||exit 1
-#./run_T4.sh || exit 1
-./run_T7.sh || exit 1
-
-
-
-
-#echo " running PhageTerm on lamda genome"
-#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Lambda_assembly.fasta
-#check_lamda_T7_res
-#ret_code=$?
-#if [ "$ret_code" -ne "0" ]; then
-#    exit $ret_code
-#fi
-#copy_lamda_T7_res res_lamda.20
-
-#echo "running PhageTerm on T7 genome"
-#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T7_assembly.fasta
-#check_StaphN1_T7_res
-#ret_code=$?
-#echo "ret_code="$ret_code
-#if [ "$ret_code" -ne "0" ]; then
-#    exit $ret_code
-#fi
-#copy_StaphN1_T7_res res_T7.20
-
-#echo "running PhageTerm on P1 genome"
-#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/P1_assembly.fasta
-#check_HK97_P1_T4_res
-#ret_code=$?
-#echo "ret_code="$ret_code
-#if [ "$ret_code" -ne "0" ]; then
-#    exit $ret_code
-#fi
-#copy_HK97_P1_T4_res res_P1.20
-
-#echo "running PhageTerm on Staph1N genome"
-#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Staph1N_assembly.fasta
-#check_StaphN1_T7_res
-#ret_code=$?
-#if [ "$ret_code" -ne "0" ]; then
-#    exit $ret_code
-#fi
-#copy_StaphN1_T7_res res_1N.20
-#
-#echo "running PhageTerm on T4 genome"
-#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T4_assembly.fasta
-#check_HK97_P1_T4_res
-#ret_code=$?
-#if [ "$ret_code" -ne "0" ]; then
-#    exit $ret_code
-#fi
-#copy_HK97_P1_T4_res res_T4.20
-#
-#echo "running PhageTerm on Virome"
-#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/virome_assembly_raw.fa
-
-
-
-
-#echo "Performing non regression tests with -l option"
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/HK97_assembly.fasta
-#if [ ! -f NA_cohesive-sequence.fasta ]; then
-#    echo "NA_cohesive-sequence.fasta does not exist!"
-#    exit 11
-#fi
-#if [ ! -f NA_PhageTerm_report.pdf ]; then
-#    echo "NA_PhageTerm_report.pdf does not exist!"
-#    exit 12
-#fi
-#if [ ! -f NA_cohesive-sequence.fasta ]; then
-#    echo "NA_cohesive-sequence.fasta does not exist!"
-#    exit 13
-#fi
-#if [ ! -f NA_statistics.csv ]; then
-#    echo "NA_statistics.csv does not exist!"
-#    exit 14
-#fi
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Lambda_assembly.fasta
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T7_assembly.fasta
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/P1_assembly.fasta
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Staph1N_assembly.fasta
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Staph1N_assembly.fasta
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T4_assembly.fasta
-#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/virome_assembly_raw.fa
-#exit 0