Customisation

The viralgenie pipeline is highly customisable, allowing you to tailor the analysis to your specific needs. This section provides information on how to customise the pipeline, including configuration options and database customisation.

Custom Databases

Viralgenie uses a variety of databases to analyse reads, contigs, and consensus constructs. While the default databases are sufficient for most cases, you can create custom databases if needed. This section provides guidance on how to create and use custom databases for different tools used in the pipeline. For more details, see the databases guide.

Custom Tool Configuration

Viralgenie allows you to modify the arguments of the tools used in the pipeline by providing a custom configuration file. This can be done by copying a segment from the modules.config file and modifying the arguments as needed. For more details, see the configuration guide.