anvi-scan-trnas

Identify and store tRNA genes in a contigs database.

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Authors

A. Murat Eren (Meren)
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Requires

contigs-db

Provides

hmm-hits

Usage

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-cutoff-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.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-scan-trnas.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-scan-trnas [-h] -c CONTIGS_DB [-T NUM_THREADS] [--log-file FILE_PATH] [--trna-hits-file FILE_PATH] [--trna-cutoff-score INT] [--just-do-it]

Parameters and their descriptions

options
-c, --contigs-db CONTIGS_DB required
Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-T, --num-threads NUM_THREADS
Maximum number of threads to use for multithreading whenever possible. Very conservatively, the default is 1, unless the environmental variable `ANVIO_THREADS` sets another positive integer. If you use this parameter, it will override `ANVIO_THREADS`. It is a good idea to not exceed the number of CPUs / cores on your system. Plus, please be careful with this option if you are running your commands on a SGE -- if you are clusterizing your runs, and asking for multiple threads to use, you may deplete your resources very fast. Default: 1
--log-file FILE_PATH
File path to store debug/output messages.
--trna-hits-file FILE_PATH
File path to store raw hits from tRNA scan.
--trna-cutoff-score INT
Minimum score to assume a hit comes from a proper tRNA gene (passed to the tRNAScan-SE). The default is 20. It can get any value between 0-100. Default: 20
--just-do-it
Don't bother me with questions or warnings, just do it.

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.

Copyleft, The anvi'o Project