diff --git a/samplesheetutils/binaries/create_samplesheet.py b/samplesheetutils/binaries/create_samplesheet.py
index d679b69..a7676a1 100644
--- a/samplesheetutils/binaries/create_samplesheet.py
+++ b/samplesheetutils/binaries/create_samplesheet.py
@@ -19,7 +19,7 @@
 logging.basicConfig()
 
 def version():
-    print("samplesheet-utils 1.3.2")
+    print("samplesheet-utils 1.3.3")
 
 #if __name__ == "__main__":
 def create_samplesheet():
@@ -85,12 +85,12 @@ def create_samplesheet():
 
     if mode == MODE_STRING_CSV:
         # Generate metadata for AA string
-        aa_sample_name = sample_name(args.aa_string.strip(), seq_chars=args.seq_chars)
+        aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars)
         aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension=args.output_extension)
         aa_path = args.fasta_dir + "/" + aa_sample_file_name
 
         # Create the fasta file
-        sample_data = Sample(aa_sample_name, aa_path, args.aa_string.strip())
+        sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split()))
         make_fasta(sample_data)
 
         # Write the samplesheet
@@ -100,12 +100,12 @@ def create_samplesheet():
 
     if mode == MODE_STRING_JSON:
         # Generate metadata for AA string
-        aa_sample_name = sample_name(args.aa_string.strip(), seq_chars=args.seq_chars)
+        aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars)
         aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension=args.output_extension)
         aa_path = args.fasta_dir + "/" + aa_sample_file_name
 
         # Create the fasta file
-        sample_data = Sample(aa_sample_name, aa_path, args.aa_string.strip())
+        sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split()))
         make_fasta(sample_data)
 
         if args.output_file == "samplesheet.csv":
@@ -117,12 +117,12 @@ def create_samplesheet():
 
     if mode == MODE_STRING_YAML:
         # Generate metadata for AA string
-        aa_sample_name = sample_name(args.aa_string.strip(), seq_chars=args.seq_chars)
+        aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars)
         aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension=args.output_extension)
         aa_path = args.fasta_dir + "/" + aa_sample_file_name
 
         # Create the fasta file
-        sample_data = Sample(aa_sample_name, aa_path, args.aa_string.strip())
+        sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split()))
         make_fasta(sample_data)
 
         if args.output_file == "samplesheet.csv":
@@ -198,13 +198,13 @@ def create_samplesheet():
             create_yaml_boltz(sample_data, ss_fp)
 
     if mode == MODE_STRING_YAML_RFAA:
-        aa_sample_name = sample_name(args.aa_string, seq_chars=args.seq_chars)
+        aa_sample_name = sample_name("".join(args.aa_string.strip().split()), seq_chars=args.seq_chars)
         # overwrite defaults
         aa_sample_file_name = file_name(aa_sample_name, prefix=args.aa_prefix, suffix=args.aa_suffix, extension="yaml")
         aa_path = args.fasta_dir + "/" + aa_sample_file_name
 
         # Create the fasta file
-        sample_data = Sample(aa_sample_name, aa_path, args.aa_string)
+        sample_data = Sample(aa_sample_name, aa_path, "".join(args.aa_string.strip().split()))
         with open(aa_sample_file_name, "w") as s_fp:
             create_yaml_rfaa(sample_data, s_fp)
 
diff --git a/samplesheetutils/binaries/truncate_msa.py b/samplesheetutils/binaries/truncate_msa.py
index ebfdfa3..055d581 100644
--- a/samplesheetutils/binaries/truncate_msa.py
+++ b/samplesheetutils/binaries/truncate_msa.py
@@ -11,7 +11,7 @@
 logging.basicConfig()
 
 def version():
-    print("samplesheet-utils 1.3.2")
+    print("samplesheet-utils 1.3.3")
 
 #if __name__ == "__main__":
 def truncate_msa():
diff --git a/setup.py b/setup.py
index 00942a4..a746e0a 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name="samplesheetutils",
-    version="1.3.2",
+    version="1.3.3",
     author="nbtm-sh",
     author_email="n.glades@unsw.edu.au",
     packages=find_packages(),