Bakta: rapid and standardized annotation of bacterial genomes via alignment- free sequence identification

Command- line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial genomes. However, results of existing command- line software pipelines heavily depend on taxon- specific databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command- line software tool for the robust, taxon- independent, thorough and, nonetheless, fast annotation of bacterial genomes. Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into account replicon metadata. The annotation of coding sequences is accelerated via an alignment- free sequence identification approach that in addition facilitates the precise assignment of public database cross- references. Annotation results are exported in GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)- compliant flat files, as well as comprehensive JSON files, facilitating automated downstream analysis. We compared Bakta to other rapid contemporary command- line annotation software tools in both targeted and taxonomically broad benchmarks including isolates and metagenomic- assembled genomes. We demonstrated that Bakta outperforms other tools in terms of functional annotations, the assignment of functional categories and database cross- references, whilst providing comparable wall- clock runtimes. Bakta is implemented in Python 3 and runs on MacOS and Linux systems. It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta. An accompanying web version is available at https://bakta.computational. bio.

Automated summary

This article introduces a new command-line software tool called Bakta for the rapid, taxon-independent annotation of bacterial genomes. Bakta outperforms other tools in terms of functional annotations, database cross-references, while providing comparable runtime.