Update file ancient_MRSA_assignment.md

assignments/ancient_MRSA_assignment.md

@@ -44,10 +44,16 @@ Quast: https://github.com/ablab/quast
 
 
 **Annotation**
+
 Prokka: https://github.com/tseemann/prokka
 
 
-**Variant calling & phylo**
+**cgMLST**
+
+Pathogen watch: https://pathogen.watch
+
+
+**Variant calling, MSA & phylo**
 
 Snippy: https://github.com/tseemann/snippy
 
@@ -55,3 +61,13 @@ Seqtk: https://github.com/lh3/seqtk
 
 IQ-Tree: http://www.iqtree.org
 
+FigTree: http://tree.bio.ed.ac.uk/software/figtree/
+
+Phandango: http://jameshadfield.github.io/phandango/#/
+
+
+**AMR & Virulence**
+
+Abricate: https://github.com/tseemann/abricate
+
+