diff --git a/dna_read.sh b/dna_read.sh
index b0d9a41e57f78772b079b114e723ffbad97a2fa2..38e8beea4bef0f5a792e79a78d1001a65434d151 100755
--- a/dna_read.sh
+++ b/dna_read.sh
@@ -128,7 +128,7 @@ then
 	n_read=$(($n_frag * 50))
 fi
 
-molecule_selection_script="$project_dir"/sequencing_simulation/select_molecules.py
+molecule_selection_script="$project_dir"/sequencing_modules/select_molecules.py
 selected_mol_path="$stored_document_path"/6_select_mol.fasta
 #select molecules from container molecules with the good primers
 call_function python3 "$molecule_selection_script" -i "$container_path"/container_molecules.fasta -o "$selected_mol_path" --start $start_primer --stop $stop_primer -n $n_read
@@ -137,7 +137,7 @@ mol_sel_time=$(date +"%s")
 #----Sequencing & Basecalling----#
 
 convert_fasta_script="$project_dir"/synthesis_simulation/dna_file_reader.py #script to convert fasta to fastq
-simu_seq_bc_script="$project_dir"/sequencing_simulation/sequencing_basecalling_simulator/sequencing_basecalling_simulator.jl
+simu_seq_bc_script="$project_dir"/sequencing_modules/sequencing_basecalling_simulator/sequencing_basecalling_simulator.jl
 sequenced_reads_path="$stored_document_path"/7_sequenced_reads.fastq
 #call_function python3 "$convert_fasta_script" "$selected_mol_path" "$sequenced_reads_path"
 call_function julia "$simu_seq_bc_script" "$selected_mol_path" "$sequenced_reads_path"
@@ -154,7 +154,7 @@ consensus_path="$stored_document_path"/8_consensus.fasta
 if [ $assembly_type == "indexed" ]
 then
 	#Clustering
-	clustering_script="$project_dir"/sequencing_simulation/clustering/clustering #script for the clustering	
+	clustering_script="$project_dir"/sequencing_modules/clustering/clustering #script for the clustering	
 	clusters_frag_dir="$stored_document_path"/8_clusters
 	
 	rm -rf "$clusters_frag_dir"
@@ -173,13 +173,13 @@ then
 	
 	#Consensus
 	
-	consensus_script="$project_dir"/sequencing_simulation/cluster_consensus.py
+	consensus_script="$project_dir"/sequencing_modules/cluster_consensus.py
 	call_function python3 "$consensus_script" "$clusters_frag_dir" "$consensus_path" $coded_frag_length
 
 else #ordered assembly
 	start_sequence=$(get_doc_param $container_path $document_index "start_sequence")
 	
-	consensus_script="$project_dir"/sequencing_simulation/reads_consensus.py
+	consensus_script="$project_dir"/sequencing_modules/reads_consensus.py
 	
 	if $channel_coding
 	then