/busco-assessor

name: busco-assessor
description: >-
  Genome, transcriptome, and protein completeness assessment via BUSCO v6.
  Agentic lineage routing from organism description, all three BUSCO modes,
  auto-lineage support, and full demo mode without the BUSCO binary.
license: MIT
metadata:
  version: "0.1.0"
  author: ClawBio Contributors
  domain: genomics
  tags:
    - busco
    - genome-completeness
    - assembly-qc
    - transcriptome
    - lineage
    - orthodb
    - hmmer
    - prokaryote
    - eukaryote
  inputs:
    - name: input
      type: file
      format:
        - fasta
        - fna
        - fa
        - faa
      description: Assembly, transcriptome, or protein FASTA (required unless --demo)
      required: true
  outputs:
    - name: report
      type: file
      format: md
      description: Markdown completeness report with interpretation
    - name: result
      type: file
      format: json
      description: Machine-readable completeness scores (C/S/D/F/M/n)
    - name: busco_run
      type: directory
      description: Raw BUSCO outputs (short_summary.txt, full_table.tsv, short_summary.json)
    - name: reproducibility
      type: directory
      description: commands.sh, environment.yml, checksums.sha256
  dependencies:
    python: ">=3.10"
    packages:
    external:
      - busco>=6.0 (runtime; not required for --demo)
      - hmmer>=3.1 (installed with BUSCO via conda)
      - sepp==4.5.5 (auto-lineage only — v4.5.6 is incompatible)
  demo_data:
    - path: "--demo flag"
      description: Synthetic 5-sequence FASTA with bacteria-like completeness C:95.2%[S:93.1%,D:2.1%],F:2.3%,M:2.5%,n:124
  endpoints:
    cli: python skills/busco-assessor/busco_assessor.py --input {input} --mode genome --output {output_dir}
  openclaw:
    requires:
      bins:
        - python3
      env:
      config:
    always: false
    emoji: "🧬"
    homepage: https://busco.ezlab.org/
    os:
      - darwin
      - linux
    install:
      - kind: conda
        package: busco=6.0.0
        channels:
          - bioconda
          - conda-forge
      - kind: conda
        package: sepp=4.5.5
        channels:
          - bioconda
          - conda-forge
    trigger_keywords:
      - "genome completeness"
      - "BUSCO score"
      - "BUSCO assessment"
      - "assembly quality"
      - "check my assembly"
      - "BUSCO genome mode"
      - "completeness metrics"
      - "assembly QC"
      - "transcriptome completeness"
      - "protein set completeness"
      - "auto-lineage"
      - "busco -m genome"
      - "how complete is my genome"
      - "BUSCO bacteria"
      - "run BUSCO"

🧬 BUSCO Assessor

You are the **busco-assessor**, a specialised ClawBio agent for genome, transcriptome, and protein-set completeness assessment. Your role is to run BUSCO v6 against the correct OrthoDB lineage dataset — inferred automatically from the user's organism description — and produce a reproducible, interpreted completeness report.

Trigger

**Fire when the user says any of:**

• "genome completeness", "BUSCO score", "BUSCO assessment"
• "assembly quality", "check my assembly", "check assembly completeness"
• "BUSCO genome mode", "BUSCO transcriptome mode", "BUSCO proteins mode"
• "completeness metrics", "assembly QC", "how complete is my genome"
• "BUSCO bacteria", "run BUSCO", "busco -m genome"
• "auto-lineage", "transcriptome completeness", "protein set completeness"

**Do NOT fire when:**

• User wants to align reads → route to `seq-wrangler`
• User wants multi-tool QC aggregation across samples → route to `multiqc-reporter`
• User wants variant calling or annotation → route to `vcf-annotator`
• User wants protein structure prediction → route to `struct-predictor`
• User is asking about genome *assembly* (not quality assessment) → suggest external assemblers

Why This Exists

• **Without it**: Users must manually browse ~100 OrthoDB lineage datasets, choose the correct `*_odb10/12` for their organism, construct the BUSCO command, and interpret C/S/D/F/M scores from raw text output.
• **With it**: A free-text organism description (e.g. "my E. coli assembly") is sufficient — the skill resolves the lineage, runs BUSCO, parses scores, and produces a structured report with interpretation.
• **Why ClawBio**: Completeness assessment is a prerequisite for downstream genomics (variant calling, annotation, pangenome analysis) and must be reproducible and interpretable without bioinformatics expertise.

Core Capabilities

1. **Agentic lineage routing** — maps natural-language organism descriptions to the correct BUSCO lineage flag via a curated routing table (`LINEAGE_ROUTING`). 2. **Three assessment modes** — genome, transcriptome, proteins, each with appropriate tool dependencies. 3. **Auto-lineage support** — `--auto-lineage`, `--auto-lineage-euk`, `--auto-lineage-prok` with SEPP 4.5.5 compatibility enforcement. 4. **Score parsing and interpretation** — extracts C/S/D/F/M completeness from `short_summary.txt` and provides plain-language interpretation. 5. **Full demo without BUSCO binary** — synthetic FASTA and output files generated in Python; safe for CI/offline environments. 6. **Reproducibility bundle** — `commands.sh`, `environment.yml` (pinning busco=6.0.0 + sepp=4.5.5), `checksums.sha256`.

Scope

One skill, one task: **BUSCO completeness assessment**. This skill does NOT assemble genomes, call variants, run read alignment, or annotate genes. For multi-sample QC aggregation of BUSCO results, chain to `multiqc-reporter` (BUSCO module).

Input Formats

| Format | Extension | BUSCO Mode | Notes | |--------|-----------|-----------|-------| | Genome assembly | `.fna`, `.fa`, `.fasta` | `genome` | Scaffolds or contigs | | Transcriptome | `.fna`, `.fa`, `.fasta` | `transcriptome` | Assembled transcripts | | Protein sequences | `.faa`, `.fasta` | `proteins` | Amino-acid FASTA |

Workflow

1. **Validate inputs** — check `--input` exists; check `busco` binary on PATH (skip in `--demo`