From b6239557b3b8040bf2ecd10b6d0522e2d0c4b9f7 Mon Sep 17 00:00:00 2001 From: Michael Hoggard <72948375+mlhoggard@users.noreply.github.com> Date: Mon, 26 Aug 2024 10:50:28 +1200 Subject: [PATCH] Update to prodigal-gv --- ...ex11_viral_taxonomy_prediction_via_vContact2.md | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md b/docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md index 04274fba..c8a1d842 100644 --- a/docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md +++ b/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//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 ```