From ee41e1695d640c33ef74bd47082faa92d81120eb Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Thu, 15 Feb 2024 10:14:20 +0100 Subject: [PATCH] Update docs/usage.md Co-authored-by: Mahesh Binzer-Panchal --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 57493523..e43d398a 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -176,7 +176,7 @@ in the workflow: the [eggNOG-mapper](http://eggnog-mapper.embl.de/) and [KofamSc Both are suitable for both prokaryotic and eukaryotic genes and both are run by default, but can be skipped using the `--skip_eggnog` and `--skip_kofamscan` options respectivelly. The tools use large databases which are downloaded automatically but paths can be provided by the user through the `--eggnog_dbpath directory` -`--kofam_dir dir` parameters respectively. +and `--kofam_dir dir` parameters respectively. A more targeted annotation option offered by the workflow is the possibility for the user to provide a set of [HMMER HMM profiles](http://eddylab.org/software/hmmer/Userguide.pdf) through the `--hmmdir dir` or `hmmfiles file0.hmm,file1.hmm,...,filen.hmm` parameters.