Include comment for sanitized single quotes
@@ -470,6 +470,9 @@ if __name__ == '__main__':
# Replace whitespaces from strain names with nothing to match Nextstrain's
# convention since whitespaces are not allowed in FASTA record names.
metadata[strain_field] = metadata[strain_field].str.replace(" ", "")
+
+ # Replace standard characters that are not accepted by all downstream
+ # tools as valid FASTA names.
metadata[strain_field] = metadata[strain_field].str.replace("'", "-")
# Rename columns as needed, after transforming strain names. This
