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Bakta Genome Annotation · jaechang-hits | DecimalAI

scienceby jaechang-hits

Bakta Genome Annotation

jaechang-hits/bakta-genome-annotation

Source jaechang-hits/sciagent-skills ↗License NOASSERTION

Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.

SkillScore86Maintained

Automatic

Research pack

Last verified 8/24/2026

What it changes

Passed 19 of 22 test cases with the skill, and 13 of 22 without it.

Without skill59%

With skill86%

Checks it passed that the model alone missed

The command uses bakta_plot.
The command specifies --dpi 300.
The command specifies amrfinder -u.

and 7 more in the full report

6 fixed13 passed either way3 still failing0 broke

Pass-rate lift: +27 pp
Tokens: +306%
Agent turns: 0%
Response time: -50%

Model gemini-3.6-flashMeasured 8/24/2026v1 · latest is v219 of 22 cases passed with skill

Tokens, turns and time describe resource use, not a dollar price.

This benchmark measured an earlier version of the skill.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/jaechang-hits-bakta-genome-annotation/SKILL.md https://app.decimal.ai/s/jaechang-hits-bakta-genome-annotation/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add jaechang-hits-bakta-genome-annotation, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/jaechang-hits-bakta-genome-annotation/ and pins it in .decimal/skills.lock

decimalai skills add jaechang-hits-bakta-genome-annotation

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/jaechang-hits-bakta-genome-annotation/SKILL.md https://app.decimal.ai/s/jaechang-hits-bakta-genome-annotation/SKILL.md

Raw file: /s/jaechang-hits-bakta-genome-annotation/SKILL.md ↗ · machine-readable summary at /s/jaechang-hits-bakta-genome-annotation.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 6

Prompt

During execution, the annotation log emitted a warning stating `AMRFinderPlus: database not up-to-date`. What command should be executed to refresh the antimicrobial resistance database?

What was checked, without and with the skill
Checked	Without skill	With skill
The command specifies amrfinder -u.	Missed	Passed

case-11 · gemini-3.6-flash · 8/24/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md602 linessingle file

Bakta Genome Annotation

Overview

Bakta is a command-line pipeline for rapid, standardized annotation of bacterial and archaeal genomes and plasmids. It combines Prodigal for CDS prediction, tRNAscan-SE/Aragorn/Barrnap/Infernal for non-coding RNA, PILER-CR/PILERCR for CRISPR detection, and a tiered DIAMOND/HMM search against a curated UniRef100 + IPS/UPS database to assign gene names, EC numbers, GO terms, and COG categories. Bakta produces NCBI-compatible outputs (GFF3, GenBank, EMBL, INSDC-formatted FASTA, plus a JSON summary and a circular Circos plot) for a typical 5 Mb genome in 5–15 minutes on 8 CPUs.

When to Use

Annotating bacterial or archaeal genome assemblies (Illumina, PacBio, Nanopore) with NCBI-compatible locus tags and product names
Annotating plasmids and other circular replicons separately with --plasmid and --complete flags
Producing JSON-structured annotation outputs that can be parsed without GenBank or GFF3 detours
Generating a publication-ready circular genome plot via the bundled bakta_plot command
Annotating MAGs (metagenome-assembled genomes) with --meta to disable Prodigal training
Use Prokka instead when you need viral/mitochondrial kingdoms or when you must reproduce a legacy Prokka pipeline exactly
Use PGAP instead when submitting to NCBI GenBank with full standards compliance
Use Bakta when you want faster runs, regularly updated UniRef-derived databases, AMRFinderPlus integration, and a JSON summary out of the box

Prerequisites

Software: Bakta ≥ 1.9, Python 3.8+, Prodigal, tRNAscan-SE, Aragorn, Barrnap, Infernal, DIAMOND, HMMER3, PILER-CR, BLAST+, AMRFinderPlus
Database: Bakta DB (full ~70 GB, or light ~3 GB) downloaded once with bakta_db download
Python packages (for output parsing): biopython, pandas, matplotlib
Input: assembled genome in FASTA format (one or more contigs)
Hardware: ≥ 16 GB RAM for full DB, ≥ 4 GB RAM for light DB; ≥ 8 CPUs recommended

Check before installing: The tool may already be available in the current environment (e.g., inside a pixi / conda env). Run command -v bakta first and skip the install commands below if it returns a path. When running inside a pixi project, invoke the tool via pixi run bakta rather than bare bakta.

# Install Bakta via conda/mamba (recommended)
mamba install -c conda-forge -c bioconda bakta

# Verify installation
bakta --version
# bakta 1.9.4

# Download the light database (~3 GB, faster, fewer functional hits)
bakta_db download --output db/ --type light

# Or full database (~70 GB, comprehensive UniRef100 coverage)
# bakta_db download --output db/ --type full

Track record

Benchmark

19 / 22

test cases passed, vs 13 / 22 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v5 — 10/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

jaechang-hits / sciagent-skills

skills/genomics-bioinformatics/annotation/bakta-genome-annotation/SKILL.md

View on GitHub ↗

License GPL-3.0Imported 10/3/2026Version v2

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

jaechang-hits/prokka-genome-annotationAnnotate 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.Close match+9 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

Bakta Genome Annotation

Overview

When to Use

Prerequisites

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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