Microbial 'omics

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anvi-scan-trnas [program]

Identify and store tRNA genes in a contigs database.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents

Can provide


Can consume



This program identifies the tRNA genes in a contigs-db and stores them in an hmm-hits.

To run, just provide a contigs-db that you want to look through.

anvi-scan-trnas -c contigs-db

Customizing the cut off score

What counts as a tRNA gene? That could be up to you.

The default minimum score for a gene to be counted is 20. However, you can set this cutoff to anywhere between 0-100. This value is actually used by the module tRNAScan-SE, so view their documentation for details. For example, to find more non-cononical tRNA genes, a user could lower the cutoff score to 10 as follows:

anvi-scan-trnas -c contigs-db \ --trna-cut-off-score 10

Other options

  • It is easy to modify where the outputs will go:

    • Use the parameter --log-file to provide a path for the output messages to go.

    • Use the parameter --trna-hits-file to provide a path for the raw tRNA scan data to go.

  • Like many anvi’o programs, you can use the tag --just-do-it to not have to look at questions or warnings

  • You can also try to multithread whenever possible by setting the --num-threads parameter (it is 1 by default). This can be used to speed up runtime, but please be aware of your system and its limitations before trying this.

Understanding the output

Essentially, the output of this program states the probability that each gene is a tRNA gene. See hmm-hits for more information.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.