diff --git a/README.md b/README.md
index 25226e0..bfe285c 100644
--- a/README.md
+++ b/README.md
@@ -57,7 +57,7 @@ To only run the isONform algorithm:<br />
 
 
 ```
-python isONform_parallel.py --fastq_folder path/to/input/files --t <nr_cores> --outfolder /path/to/outfolder --split_wrt_batches 
+isONform_parallel --fastq_folder path/to/input/files --t <nr_cores> --outfolder /path/to/outfolder --split_wrt_batches 
 ```
 
 Note: Please always give absolute paths to the files or folders
diff --git a/full_pipeline.sh b/full_pipeline.sh
deleted file mode 100755
index 426d52c..0000000
--- a/full_pipeline.sh
+++ /dev/null
@@ -1,105 +0,0 @@
-#!/bin/bash
-set -e
-#if [ $# -ne 6 ]; then
-#        echo "Usage: `basename $0`  <raw_reads.fq>  <outfolder>  <num_cores> <isONform_folder> <iso_abundance> <mode> "
-#        exit 0
-#fi
-#the pipeline can be run in different modes:
-# full: the full pipeline is run (pychopper, isONclust,isONcorrect,isONform)
-# pacbio: for PacBio data runs isONclust and isONform
-# ont: analysis of ont data:  isONclust,isONcorrect and isONform are run
-# only_isonform: only isONform is run
-raw_reads=$1
-outfolder=$2
-num_cores=$3
-isONform_folder=$4
-iso_abundance=$5
-mode=$6
-echo "Running: " `basename $0` $raw_reads $outfolder $num_cores $isONform_folder $iso_abundance $mode
-isonform_folder=${isONform_folder::-1}
-mkdir -p $outfolder
-#conda init bash
-#conda activate /proj/snic2022-6-31/nobackup/alexp/conda_envs/isonform
-if [ $mode == "full" ]
-then
-echo
-echo "Will run pychopper (cdna_classifier.py), isONclust, isONcorrect and isONform. Make sure you have these tools installed."
-echo "For installation see: https://github.com/ksahlin/isONcorrect#installation and  https://github.com/aljpetri/isONform"
-echo
-
-echo
-echo "Running pychopper"
-echo
-
-pychopper  $raw_reads $outfolder/full_length.fq -t $num_cores
-
-echo
-echo "Finished pychopper"
-echo
-
-fi
-
-echo
-echo "Running isONclust"
-echo
-if [ $mode != "only_isonform" ]
-then
-if [ $mode != "pacbio" ] && [ $mode != "'ont'" ]
-then
-/usr/bin/time -v isONclust  --t $num_cores  --ont --fastq $outfolder/full_length.fq \
-             --outfolder $outfolder/clustering
-/usr/bin/time -v isONclust write_fastq --N $iso_abundance --clusters $outfolder/clustering/final_clusters.tsv \
-                      --fastq $outfolder/full_length.fq --outfolder  $outfolder/clustering/fastq_files
-elif [ $mode == "ont" ]
-then
-/usr/bin/time -v  isONclust  --t $num_cores  --ont --fastq $raw_reads \
-             --outfolder $outfolder/clustering
-/usr/bin/time -v isONclust write_fastq --N $iso_abundance --clusters $outfolder/clustering/final_clusters.tsv \
-                      --fastq $raw_reads --outfolder  $outfolder/clustering/fastq_files
-#The mode is pacbio here
-else
-/usr/bin/time -v  isONclust  --t $num_cores  --isoseq  --fastq $raw_reads \
-             --outfolder $outfolder/clustering
-/usr/bin/time -v isONclust write_fastq --N $iso_abundance --clusters $outfolder/clustering/final_clusters.tsv \
-                      --fastq $raw_reads --outfolder  $outfolder/clustering/fastq_files
-fi
-
-echo
-echo "Finished isONclust"
-echo
-#conda activate isON311
-
-if [ $mode != "pacbio" ]
-then
-  echo
-  echo "Running isONcorrect"
-  echo
-
- /usr/bin/time -v python3.11 run_isoncorrect --t $num_cores  --fastq_folder $outfolder/clustering/fastq_files  --outfolder $outfolder/correction/
-
-  echo
-  echo "Finished isONcorrect"
-  echo
-fi
-fi
-echo
-echo "Merging reads back to single file. Corrected reads per cluster are still stored in: " $outfolder/correction/
-echo
-
-echo
-echo "Running isONform"
-echo
-if [ $mode != "pacbio" ]
-then
-/usr/bin/time -v python3.11 $isONform_folder/isONform_parallel.py --t $num_cores  --fastq_folder $outfolder/correction/ --exact_instance_limit 50 --k 20 --w 31 --xmin 14 --xmax 80 --max_seqs_to_spoa 200 --delta_len 10 --outfolder $outfolder/isoforms --iso_abundance $iso_abundance --split_wrt_batches  --delta_iso_len_3 30 --delta_iso_len_5 50
-else #run isONform in ont or only_isONform mode
-/usr/bin/time -v  python3.11 $isONform_folder/isONform_parallel.py --t $num_cores --fastq_folder $outfolder/clustering/fastq_files --exact_instance_limit 50 --k 20 --w 31 --xmin 14 --xmax 80 --max_seqs_to_spoa 200 --delta_len 10 --outfolder $outfolder/isoforms --iso_abundance $iso_abundance --split_wrt_batches --delta_iso_len_3 30 --delta_iso_len_5 50 --clustered
-fi
-echo
-echo "Finished isONform"
-echo
-
-echo
-echo "Finished with pipeline and wrote corrected reads to: " $outfolder
-echo
-