Prokanota v2.0.0: A new flexible foundation for prokaryotic annotation
Prokanota 2.0 fundamentally rebuilds the pipeline to make prokaryotic annotation more flexible, extensible, and reliable. Database integrations are no longer tied to a fixed workflow: supported searches can be configured and combined while producing consistent, interoperable annotation outputs.
Highlights
- Configure HMM, RPS-BLAST, BLAST-formatted protein, DIAMOND, and MMseqs2 databases without editing the Snakemake workflow; rules are generated dynamically for the enabled databases.
- Annotate genomes, precomputed protein collections, or both in the same run.
- Produce standardized annotation tables alongside richer GFF3, GenBank, FASTA, and TSV outputs with deterministic identifiers and retained biological metadata.
- Use a packaged command-line interface for configuration, validation, execution, testing, and common setup tasks while retaining direct Snakemake compatibility.
- Benefit from stricter input and configuration validation, safer path handling, clearer logging, reproducible packaging, and substantially expanded automated regression and targeted biological validation.
Upgrading
Because 2.0 changes the architecture, configuration model, identifiers, and parts of the output contract, users upgrading from Prokanota 1.x should generate fresh configuration templates and review downstream assumptions before switching existing analyses.
Full Changelog: 1.2.0...2.0.0