From ece558a3b8cb0717113e8405708da438d550a44c Mon Sep 17 00:00:00 2001 From: Torsten Seemann Date: Mon, 11 Nov 2019 18:29:45 +1100 Subject: [PATCH] Add --prodigaltf to docs --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index b4e0f26..88b20be 100644 --- a/README.md +++ b/README.md @@ -209,6 +209,7 @@ $HOME/prokka/bin/prokka --setupdb Annotations: --kingdom [X] Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria') --gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0') + --prodigaltf [X] Prodigal training file (default '') --gram [X] Gram: -/neg +/pos (default '') --usegenus Use genus-specific BLAST databases (needs --genus) (default OFF) --proteins [X] Fasta file of trusted proteins to first annotate from (default '') @@ -239,6 +240,13 @@ use of Genbank is recommended over FASTA, because it will provide `/gene` and `/EC_number` annotations that a typical `.faa` file will not provide, unless you have specially formatted it for Prokka. +### Option: --prodigaltf + +Instead of letting `prodigal` train its gene model on the contigs you +provide, you can pre-train it on some good closed reference genomes first +using the `prodigal -t` option. Once you've done that, provide `prokka` +the training file using the `--prodgialtf` option. + ### Option: --rawproduct Prokka annotates proteins by using sequence similarity to other proteins in its database,