diff --git a/README.md b/README.md
index 95b3679..176fca6 100644
--- a/README.md
+++ b/README.md
@@ -33,6 +33,7 @@ positional arguments:
 optional arguments:
   -h, --help            show this help message and exit
   --csv_N               Include Ns in sample variant CSVs
+  --no_trim_terminal_N  Don't trim Ns from sequence terminus. Default behaviour is to trim Ns and gaps BEFORE analysis
   --no_gzip_json        Don't gzip typing JSON files
   --output_unclassified
                         Retain unclassified samples in summary CSV
diff --git a/aln2type/aln2type.py b/aln2type/aln2type.py
index 93ae619..3e9505a 100644
--- a/aln2type/aln2type.py
+++ b/aln2type/aln2type.py
@@ -573,6 +573,9 @@ def write_sample_variant_csv(name, variants, sample_csv_outdir, csv_N=False):
 def remove_terminal_gapns(seq):
     return re.sub(r'(N|-)*$', '', seq)
 
+def remove_terminal_gaps(seq):
+    return re.sub(r'-*$', '', seq)
+
 def go(args):
 
     refseq = get_ref_seq(args.msa, args.ref_name)
@@ -592,7 +595,10 @@ def go(args):
             if name == args.ref_name:
                 continue
             else:
-                variants = update_variants(remove_terminal_gapns(seq.upper()), refseq)
+                if args.no_trim_terminal_N:
+                    variants = update_variants(remove_terminal_gaps(seq.upper()), refseq)
+                else:
+                    variants = update_variants(remove_terminal_gapns(seq.upper()), refseq)
 
                 print(name)
                 if variants:
diff --git a/aln2type/cli.py b/aln2type/cli.py
index 1506a62..bae59e6 100644
--- a/aln2type/cli.py
+++ b/aln2type/cli.py
@@ -4,6 +4,7 @@
 def parse_args():
     parser = argparse.ArgumentParser()
     parser.add_argument("--csv_N", action='store_true', required=False, help="Include Ns in sample variant CSVs")
+    parser.add_argument("--no_trim_terminal_N", action='store_true', required=False, help="Don't trim Ns from sequence terminus. Default behaviour is to trim Ns and gaps BEFORE analysis")
     parser.add_argument("--no_gzip_json", action='store_true', required=False, help="Don't gzip typing JSON files")
     parser.add_argument("--output_unclassified", action='store_true', required=False, help="Retain unclassified samples in summary CSV")
     parser.add_argument("--no_call_deletion", action='store_true', required=False, help="Allow deleted positions to be treated as no-calls not ref")
diff --git a/aln2type/version.py b/aln2type/version.py
index 3b93d0b..27fdca4 100644
--- a/aln2type/version.py
+++ b/aln2type/version.py
@@ -1 +1 @@
-__version__ = "0.0.2"
+__version__ = "0.0.3"