Bakta Command Line

This chapter describes the usage of the main Bakta command line tool (CLI). It is derived from the official README.md on GitHub.

The following sections describe the overall usage of the Bakta CLI:

• Installation - How to install Bakta
• Examples - Basic usage examples
• Input and Output - Information about input and output files
• Usage - Command Line Options
• Annotation Workflow - Technical details about the annotation workflow
• Database - How to prepare and use the mandatory database
• Genome Submission - How to submit genomes to common repositories
• Protein bulk annotation - Bulk annotation of proteins
• Genome plots - Configuration options for creating genome plots
• Auxillary scripts - Additional helper scripts that might be useful
• Citation - How to cite the tool in your own work
• FAQ - A few frequently askes questions