Conserved modules

From version 1.2.0, it is possible to predict and work with conserved modules using PPanGGOLiN. Modules are groups of genes that are part of the variable genome, and often found together in the different genomes. As such, they are conserved modules and potential functional modules.

This tool can be used using the ppanggolin panmodule command directly from your .fasta or .gbff file lists instead of the ppanggolin workflow command. It will run additional analysis related to module predictions only, with some more descriptive files related to modules.

The analysis can also be run directly on your formerly computed pangenomes with a dedicated subcommand.

Module

Once partitions have been computed, you can predict conserved modules. All of the options of the module subcommand are for tuning the parameters for the analysis. Details about each parameter and what they do is available in the related preprint.

The command can be used simply as such:

ppanggolin module -p pangenome.h5

This will predict modules and store the results in the HDF5 file. If you wish to have descriptive tsv files, whose format is detailed here, you can use:

ppanggolin write -p pangenome.h5 --modules --output MYOUTPUTDIR.

If your pangenome has spots of insertion that were predicted using the spot command (or the panrgp or all commands), you can also list the associations between the predicted spots and the predicted modules as such:

ppanggolin write -p pangenome.h5 --spot_modules --output MYOUTPUTDIR

The format of each file is given here