prokka-genome-annotation

# Prokka Genome Annotation ## Overview Prokka is a command-line pipeline for rapid annotation of prokaryotic genomes (bacteria, archaea, and viruses). It uses a tiered search strategy: protein-coding genes (CDS) are predicted with Prodigal and searched first against a genus-specific database, then RefSeq proteins, then Pfam/TIGRFAMs HMMs. Non-coding RNA genes (rRNA, tRNA, tmRNA) are identified with Barrnap, Aragorn, and Infernal. Prokka processes a single FASTA assembly in minutes and outputs a comprehensive annotation in GFF3, GenBank, FASTA, and tabular formats. ## When to Use - Annotating a newly assembled bacterial or archaeal genome from Illumina, PacBio, or Nanopore assemblies - Getting functional protein annotations (CDS with product names, EC numbers, GO terms) from a draft or complete genome - Preparing annotation files for downstream comparative genomics (Roary pan-genome, OrthoFinder) - Annotating viral or phage genomes when kingdom-specific databases are important - Performing metagenome-assembled genome (MAG) annotation with the `--metagenome` flag - Parsing annotated outputs in Python with BioPython for downstream sequence or feature analysis - Use **PGAP** (NCBI Prokaryotic Genome Annotation Pipeline) instead when the goal is NCBI GenBank submission with standards compliance - Use **Bakta** instead for faster annotation with built-in NCBI-compatible outputs and a more regularly updated database ## Prerequisites - **Software**: Prokka ≥ 1.14, Perl 5, Prodi...