The DOI matches its Crossref record; 52 of the 52 references it cites were found in a registry or an index.
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification: Find out more about Bakta, the motivation, challenges and applications, here.
Open accessAbstract
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 .
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Zhernakova, D. V., Wang, D., Liu, L., Andreu-Sánchez, S., Zhang, Y., Ruiz-Moreno, A. J., Peng, H., Plomp, N., Del Castillo-Izquierdo, Á., Gacesa, R., et al. (2024) · Nature · doi:10.1038/s41586-023-06893-w · Cited by 174
BFVD—a large repository of predicted viral protein structures
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AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics
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Self-citationProtein structure-informed bacteriophage genome annotation with Phold
Bouras, G., Grigson, S. R., Mirdita, M., Heinzinger, M., Papudeshi, B., Mallawaarachchi, V., Green, R., Kim, R. S., Mihalia, V., Psaltis, A. J., et al. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkaf1448 · Cited by 71
Metadata
- Authors
- Schwengers, O., Jelonek, L., Dieckmann, M. A., Beyvers, S., Blom, J., & Goesmann, A.
- Venue
- Microbial Genomics
- Publisher
- Microbiology Society
- Published
- 2021-11-30
- Volume
- 7
- Issue
- 11
- ISSN
- 2057-5858 (ISSN-L)
- OpenAlex
- W3209528471
- Cited by
- 1,424
- References
- 52
- FWCI
- 32.34
- Type
- journal article
- Language
- en
- Open access
- gold
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