Recent updates on Bakta - a rapid & standardized software tool for the comprehensive annotation of bacterial genomes

Introduction
A thorough genome annotation has become key for many downstream analyses. However, focus has shifted from manual annotations of single genomes to high-throughput batch annotations. Addressing these challenges, we recently published Bakta - a command line software tool for the annotation of bacterial genomes, MAGs and plasmids. Here, we present new developments, added features and improvements.

Goals
We improved the performance of our software including better annotation results, technical maintenance, supporting common standards, and addressing the various feedback and requests of our active users.

Results
New features and enhancements have been added improving annotation results and overall software usability. First, we introduced the detection of pseudogenes. A new workflow detects conserved sequences located around de novo-predicted genes and screens elongated alignments for pseudogenization events or hints for translational exceptions. Second, Bakta now supports the annotation of MAGs adjusting internal gene prediction parameters. Third, we updated a the mandatory database incorporating the latest releases of public databases. Fourth, for the annotation of special-interest genes, an import of user-provided protein sequences has been implemented. Fifth, since de novo gene prediction tools fail to correctly predict translational exceptions, we developed a module to detect and annotate selenocysteine proteins by taking advantage of specific ncRNA motifs. Sixth, to manually correct gene coordinates, user can provide trusted feature coordinates in Genbank or GFF format. Seventh, for the streamlined bulk annotation of protein sequences only, we added a new sub command that can be used in addition to the actual whole-genome annotation pipeline. Last but not least, many enhancements have been added in terms of quality, maintenance and usability of the software following feedback and requests from the community.

Summary
We present various improvements of Bakta. This includes important new features and various usability improvements supported by the comprehensive feedback from our active user community.