IdentifyParalogousLoci - Tutorial

Objective

This tutorial will show you how to identify paralogous loci in a schema using the IdentifyParalogousLoci module.

Prerequisites

Download the schema from chewBBACA’s tutorial.

Procedure

Open a terminal window.
Modify the following command and run it to identify paralogous loci in a schema:

SR IdentifyParalogousLoci -s 'path/to/tutorial_schema/schema_seed' -o 'path/to/files/output_folder/IdentifyParalogousLoci_Results' -tt 11 -c 6 -pm alleles_vs_alleles

Important

Replace path/to/files/ with the actual path to the files.

Check the output directory for the list of identified paralogous loci. The first lines of the file containing the list of clusters of paralogous loci that were identified should look like:

Loci_id     Action
GCA-000007265-protein1932   Join
GCA-000730215-protein1962   Join
#
GCA-000427055-protein1391   Join
GCA-000427035-protein1421   Join
GCA-000782855-protein1355   Join
#
GCA-000012705-protein2017   Join
GCA-000427075-protein2050   Join
#

Example Output Structure

To see the expected output structure, refer to the “Outputs” section in the IdentifyParalogousLoci documentation.

Conclusion

You have successfully identified paralogous loci in a schema using the IdentifyParalogousLoci documentation module.