prokka-genome-annotation
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.
npx skills add BioTender-max/awesome-bio-agent-skills --skill prokka-genome-annotation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Annotates prokaryotic genomes using Prokka's BLAST/HMM pipeline, identifying CDS, rRNA, tRNA, tmRNA, and signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, and TSV. Encourages using PGAP for NCBI GenBank submission and Bakta for faster NCBI-compatible annotation.
How it works
- Installs and verifies Prokka and its dependencies (Prodigal, Barrnap, HMMER3, BLAST+, Aragorn, Infernal, tbl2asn).
- Prepares input genome FASTA; renames headers to Prokka-compatible contig IDs.
- Runs Prokka with options for bacterial genomes, including genus/species hints to select genus-specific databases, and sets CPU/policing like --cpus and --mincontiglen.
- Produces outputs in annotation/ with files like E_coli_K12.gbk, E_coli_K12.gff, E_coli_K12.tsv, E_coli_K12.faa, E_coli_K12.ffn, and log files.
- Includes steps to parse the TSV summary, GenBank, and protein FASTA for downstream analyses and cross-strain comparisons.
- Provides batch annotation and summary collection scripts to process multiple genomes and to compare strain protein sets.
When to use it
- Annotating newly assembled bacterial/archaeal genomes from Illumina, PacBio, or Nanopore.
- Generating functional CDS annotations with product names, EC numbers, and GO terms.
- Preparing files for downstream comparative genomics or submitting to GenBank via PGAP; Bakta recommended for faster, compatible outputs.
- Annotating viral or phage genomes when relevant databases are needed.
- MAG annotation with the --metagenome flag.
What it can touch
- Prokka executable and dependencies (Prokka and its toolchain) as installed in the environment.
- Input genome FASTA; output directory annotation/ with multiple result files including .gff, .gbk, .faa, .ffn, .gbk, .tsv, and .txt.
- Optional: Python and plotting libraries for parsing and visualization (Biopython, pandas, matplotlib).
Caveats
- Requires Prokka ≥ 1.14 and a set of dependencies; environment must provide BLAST+, HMMER, Barrnap, Aragorn, Infernal, and tbl2asn.
- Outputs depend on genome quality and database availability; specific results (counts of CDS, rRNA, tRNA) are not guaranteed and depend on input data and parameters.
# 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 Prok
- Overview
- When to Use
- Prerequisites
- Quick Start
- Workflow
- Step 1: Install and Verify Prokka
- Step 2: Prepare the Input Genome
- Step 3: Run Basic Prokka Annotation
- Step 4: Parse Annotation Summary (TSV)
- Step 5: Parse GenBank Output with BioPython
- Step 6: Visualize Annotation Statistics
- Step 7: Batch Annotation Across Multiple Genomes
- Step 8: Compare Annotations Between Strains
- Key Parameters
Install Prokka via conda/mamba (recommended) conda install -c conda-forge -c bioconda prokka Or with mamba (faster) mamba install -c conda-forge -c bioconda prokka Verify installation and database setup prokka --version prokka 1.14.6 Check that required tools are on PATH prokka --depends prokka needs: awk, sed, grep, makeblastdb, blastp, hmmscan, ...
What does the prokka-genome-annotation skill do?
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill prokka-genome-annotation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 144 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.