Designing mechanisms into Bactopia to support its users and contribute back to the community

Bactopia is a Nextflow pipeline for the complete analysis of bacterial genomes. Users can process Illumina and/or Nanopore sequences with more than 150 open-source bioinformatic tools and publicly available datasets. Furthermore, 50 additional workflows, called Bactopia Tools, are available for downstream comparative analyses, such as pan-genome, phylogenetic and functional analyses.

We designed Bactopia to help support and contribute back to the bioinformatics community. To include a tool in Bactopia, it must be available on Bioconda, and all Bactopia Tools must be available from nf-core/modules. By implementing these design principles, we have been able to make more than 140 contributions back to the wider bioinformatic community.

Bactopia is written in DSL2 following nf-core practices and is easily accessed through Bioconda, Docker, and Singularity. Documentation and code are available at https://bactopia.github.io/.