PPanGGOLiN can predict and work with conserved modules, which are groups of genes that are part of the variable genome, and often found together across the genomes of the pangenome. These conserved modules may also be potential functional modules.

--- title: "Workflow Overview: Steps launched by the panmodule command" align: center --- %%{init: {'theme':'default'}}%% graph LR i[input genomes] --> a m:::panmodule subgraph Pangenome creation a:::workflow c:::workflow g:::workflow p:::workflow a("annotate") --> c c(cluster) --> g(graph) g(graph) --> p(partition) end subgraph Functional module p --> m(module) end p --> f[pangenome.h5] m --> f classDef panrgp fill:#4066d4 classDef panmodule fill:#d44066 classDef workflow fill:#d4ae40

Further details can be found in the panModule preprint

The panModule workflow

The panModule workflow facilitates the generation of a pangenome with predicted conserved modules from a specified set of genomes. This command extends the functionality of the workflow command by detecting conserved modules. Additionally, it generates descriptive tsv files detailing the predicted modules, whose format are detailed here.

To execute the panModule workflow, use the following command:

ppanggolin panmodule --fasta GENOME_LIST_FILE

Replace GENOME_LIST_FILE with a tab-separated file listing the genome names, and the fasta file path of their genomic sequences as described here. Alternatively, you can provide a list of GFF/GBFF files as input by using the --anno parameter, similar to how it is used in the workflow and annotate commands.

The panmodule workflow predicts modules using default parameters. To fine-tune the detection, you can use the module command on a partitioned pangenome acquired through the workflow for example or use a configuration file, as described here.

Predict conserved module

The module command predicts conserved modules on an partitioned pangenome. The command has several options for tuning the prediction. Details about each parameter are 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 pangenome file. If you wish to have descriptive tsv files, whose format is detailed here, you can use the write_pangenome command with the flag --modules:

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

If spots of insertion have been predicted in you pangenome using the spot command (or inside the panrgp or all workflow commands), you can also list the associations between the predicted spots and the predicted modules as such:

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

The format of each file is given here