Prokka

Prokka is an open-source software tool designed for the rapid annotation of prokaryotic genomes, including bacteria and archaea. It automates the process of identifying genes and other features and assigning provisional functions, producing annotation files suitable for downstream analysis and submission to public databases.

The program integrates several established components to annotate a genome. Gene prediction is performed with Prodigal, which identifies coding sequences and predicts coordinate information. Transfer RNA genes are detected with Aragorn, while ribosomal RNA genes are identified using Barrnap. Functional annotation is inferred by comparing predicted proteins to curated protein databases, and users can supply their own protein sequences to guide or refine annotation. Prokka can also annotate features such as tmRNA, signal peptides, and other genetic elements, and it assigns locus tags to produced features for consistent downstream referencing.

Input to Prokka is typically a single assembled genome in FASTA format, and the output is organized in a dedicated directory. Key outputs include a GenBank file (GBK) with full feature annotations, gene and protein FASTA files (FAA and FNA), a General Feature Format (GFF3) file, a nucleotide sequence table (tbl), and a summary report. Users can customize the annotation with options for genus, species, strain, and whether to use a custom protein database, and can specify the number of CPU cores for parallel processing.

Prokka has become a widely adopted tool in microbial genomics due to its speed, ease of use, and ability to produce standard-format annotation suitable for genome papers and database submissions. It is available as open-source software and is distributed through common bioinformatics channels and package managers.