Journal article

Authors list: Schwengers, Oliver; Jelonek, Lukas; Dieckmann, Marius Alfred; Beyvers, Sebastian; Blom, Jochen; Goesmann, Alexander

Publication year: 2021

Journal: Microbial Genomics

Volume number: 7

Issue number: 11

ISSN: 2057-5858

Open access status: Gold

DOI Link: https://doi.org/10.1099/mgen.0.000685

Publisher: Microbiology Society

Abstract: 

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.

Harvard Citation style: Schwengers, O., Jelonek, L., Dieckmann, M., Beyvers, S., Blom, J. and Goesmann, A. (2021) Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification, Microbial Genomics, 7(11), Article 000685. https://doi.org/10.1099/mgen.0.000685

APA Citation style: Schwengers, O., Jelonek, L., Dieckmann, M., Beyvers, S., Blom, J., & Goesmann, A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics. 7(11), Article 000685. https://doi.org/10.1099/mgen.0.000685