Update to prodigal-gv

docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md

@@ -1,6 +1,12 @@
 # APPENDIX (ex11) : Viral taxonomy prediction via *vContact2*
 
-## 1. Predict genes via `prodigal`
+## 1. Predict genes via *prodigal-gv*
+
+Prodigal-gv is a variant of prodigal that has been modified to improve gene calling for giant viruses and viruses that use alternative genetic codes. More information is available [here](https://github.com/apcamargo/prodigal-gv).
+
+!!! note "Note"
+
+    If you have already run DRAM-v to annotate viral genes, DRAM-v runs prodigal-gv in the background, so you can also use the genes.faa file generated by DRAM-v as input for vConTACT2 here.
 
 !!! terminal "code"
 
@@ -34,13 +40,13 @@ Example slurm script:
 
     # Load dependencies
     module purge
-    module load prodigal/2.6.3-GCC-11.3.0
+    module load prodigal-gv/2.9.0-GCC-11.3.0
 
     # Set up working directories
     cd /nesi/nobackup/nesi02659/MGSS_U/<YOUR FOLDER>/7.viruses
 
-    # Run Prodigal to predict genes 
-    prodigal -p meta -q \
+    # Run Prodigal-gv to predict viral genes 
+    prodigal-gv -p meta -q \
              -i checkv_combined.fna \
              -a viral_taxonomy/checkv_combined.faa 
     ```