diff --git a/amrfinder.cpp b/amrfinder.cpp
index 2569309..442842b 100644
--- a/amrfinder.cpp
+++ b/amrfinder.cpp
@@ -357,7 +357,7 @@ struct ThisApplication : ShellApplication
       addKey ("dir", "Common directory of the --protein, --nucleotide and --gff files", "", '\0', "DIRECTORY");
     #endif
     	addKey ("protein", "Input protein FASTA file (can be gzipped)", "", 'p', "PROT_FASTA");
-    	addKey ("nucleotide", "Input nucleotide FASTA file (can be gzipped)", "", 'n', "NUC_FASTA");
+    	addKey ("nucleotide", "Input assembled nucleotide FASTA file (can be gzipped)", "", 'n', "NUC_FASTA");
     	addKey ("gff", "GFF file for protein locations (can be gzipped). Protein id should be in the attribute 'Name=<id>' (9th field) of the rows with type 'CDS' or 'gene' (3rd field).", "", 'g', "GFF_FILE");
 
       {    	
diff --git a/stxtyper b/stxtyper
index 885db86..cdcc132 160000
--- a/stxtyper
+++ b/stxtyper
@@ -1 +1 @@
-Subproject commit 885db860b184cfd8dbec46d99bdc11b1516d38b6
+Subproject commit cdcc13248ebd5576ac4002d2f6a6fafd1582d594