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Update docs/usage.md
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Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
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danilodileo and mahesh-panchal authored Feb 15, 2024
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Expand Up @@ -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.
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