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          @article{mbs:/content/journal/mgen/10.1099/mgen.0.000685,
   author = "Schwengers, Oliver and Jelonek, Lukas and Dieckmann, Marius Alfred and Beyvers, Sebastian and Blom, Jochen and Goesmann, Alexander",
   title = "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification",
   journal= "Microbial Genomics",
   year = "2021",
   volume = "7",
   number = "11",
   pages = "",
   doi = "https://doi.org/10.1099/mgen.0.000685",
   url = "https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000685",
   publisher = "Microbiology Society",
   issn = "2057-5858",
   type = "Journal Article",
   keywords = "whole-genome sequencing",
   keywords = "bacteria",
   keywords = "metagenome-assembled genomes",
   keywords = "plasmids ",
   keywords = "genome annotation",
   eid = "000685",
   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.",
  }
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