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prokaryotic-annotation

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Annotates bacterial and archaeal genomes (isolates, MAGs, plasmids) with Bakta (active versioned databases, NCBI-compliant output) or Prokka (legacy), producing GFF3/GenBank/EMBL/FASTA with INSDC locus tags. Covers Bakta-vs-Prokka-vs-PGAP-vs-DFAST choice, light-vs-full database tiers, translation-table selection (11/4/25), archaeal and leaderless-gene caveats, the small-ORF blind spot, pseudogene-vs-phase-variation, the pangenome re-annotation trap, and submission compliance. Use when annotating a newly assembled prokaryotic genome, choosing an annotation tool, re-annotating a collection for pangenomics, or preparing annotations for NCBI/DDBJ submission.

When to use

• Annotating newly assembled prokaryotic genomes
• Choosing annotation tools
• Re-annotating collections for pangenomics
• Preparing annotations for NCBI/DDBJ submission
• Annotating MAGs and plasmids
• Selecting translation tables
• Handling archaeal and leaderless-gene caveats

When not to use

• Genome assembly
• Assembly QC

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