Bactopia Roadmap and TODOs

[rpetit3]

Bactopia is continuously being updated and there are still many things on the roadmap. To be more transparent, I'll document what's planned and what needs to be done. Feel free to make suggestions, and if it's within the scope of Bactopia I'll add it to the list here.

Please keep in mind, at the moment it is just myself maintaining Bactopia, so I cannot guarantee any of these will be implemented. If you want a guarantee, consider contributing to Bactopia, because teamwork makes the dreamwork!

Bug Fixes

• Large database downloads
• Roary of Mac (likely related to perl shebang in dependencies)
• hybrid assembly with short polishing

New Features

• check for contamination
• pick datasets based on taxonomic classifications
• summary table in TSV
• MultiQC based report
• revamped CLI
• prophage identification
• Terra.bio integration
• CGC integration

Documentation

• Add ONT examples
• update docs to most recent version
• version controlled docs (e.g. see docs at time of v2.0.1)
• docs to help get started developing Bactopia ([question] How to set up a copy of Bactopia for development #353)
• how to run on HPC with singularity
• running on the cloud (AWS, GCP, Azure)

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This has been modeled after rust-bio's Roadmap/Todos, thank you Johannes!

[plasmid02]

I think a feature where you can enter a sketch of existing species diversity and only process new genomes that are n % distant from exisiting strains. ie only process samples that are dissimilar to those I have already processed