# Build BUSCO Phylogenies from Genome Assemblies

Genome-to-tree phylogenomics requires many tools, file transformations, and scheduler settings. This skill creates a tailored BUSCO/compleasm workflow with scripts, quality checks, tree inference, and methods text.

## Install

```bash
npx skillstore add brunoasm/busco-phylogeny
```

## Metadata

- Status: approved
- Slug: brunoasm-busco-phylogeny
- Skillstore revision: r2
- Version status: missing
- Tree hash: 204671e8eb2d8fb79a6314314f7fa42a987ae0c958c51b6468312d2dc85a94be
- Author: brunoasm
- GitHub username: brunoasm
- License: MIT
- Repository: https://github.com/brunoasm/my\_claude\_skills/tree/main/phylo\_from\_buscos
- Ref: a39a91716eadede5f4cdefd78178fed4e837a128
- Supported tools: Claude, Codex, Claude Code
- Audit status: complete
- Agent install advisory: confirmation\_required
- Manual install advisory: allowed
- Artifact signature: available
- Audit attestation: unavailable
- Human verification: not\_verified
- Risk factors: external\_commands, network, filesystem
- Quality score: 38
- Quality tier: warning
- Public page: https://skillstore.pages.dev/skills/brunoasm-busco-phylogeny
- Manifest: https://skillstore.pages.dev/api/skills/brunoasm-busco-phylogeny/manifest

## Capabilities

- Queries NCBI assemblies by taxon and filters results by assembly level, annotation, RefSeq status, and contig N50.
- Downloads selected NCBI genomes through the datasets CLI and prepares accession-based inputs.
- Generates local, SLURM, or PBS scripts for compleasm, alignment, trimming, partition search, and gene-tree inference.
- Extracts single-copy orthologs, creates QC summaries, and converts FASconCAT partition data for IQ-TREE.
- Supports trimAl, ClipKit, BMGE, or Aliscore/ALICUT trimming workflows.
- Produces concatenated and ASTRAL tree workflows plus a customized publication methods paragraph.

## Use Cases

- Plan a Comparative Genomics Study: Turn selected genome assemblies into a documented ortholog, alignment, trimming, and tree-inference workflow.
- Prepare Cluster Jobs: Generate resource-aware SLURM or PBS scripts with array jobs for large genome and locus collections.
- Learn Phylogenomics: Follow each genome-to-tree stage with quality thresholds, method choices, expected outputs, and publication guidance.

## Prompt Templates

### Create a Local Workflow

```
Create a local BUSCO phylogeny workflow for [taxon] using [genome paths]. Ask for missing lineage, CPU, memory, and trimming choices.
```

### Select NCBI Assemblies

```
Find up to [count] NCBI assemblies for [taxon]. Prioritize [quality criteria], show quality metrics, and prepare selected accessions for download.
```

### Generate Cluster Scripts

```
Generate SLURM scripts for [genome count] genomes using [BUSCO lineage], [CPU count] CPUs, [memory], and [walltime]. Use array jobs where appropriate.
```

### Design and Validate an Analysis

```
Design and validate a complete workflow for [taxon]. Compare [trimming methods], test [model set], infer concatenated and ASTRAL trees, and draft methods text.
```

## Limitations

- Requires external bioinformatics tools, a supported scheduler or local shell, and adequate compute resources.
- Does not complete an analysis without user-provided genomes, taxonomy, resources, and software choices.
- Network-dependent steps require NCBI access and may download third-party tools or reference data.
- Generated scripts require review because file paths, scheduler policies, software versions, and dataset sizes vary.

## Best Practices

- Review generated paths, resource requests, software versions, and scheduler directives before execution.
- Use consistent sample names and retain accession mappings, QC reports, logs, parameters, and intermediate files.
- Pin and verify downloaded tools, then test the workflow on a small genome subset before scaling.

## Anti Patterns

- Do not mix unrelated BUSCO lineages or inconsistent assembly-quality thresholds without documenting the rationale.
- Do not submit large job arrays before validating one genome and one locus end to end.
- Do not run mutable downloaded scripts or installers without version pinning and integrity verification.

## Security Audit

- Audited at: 2026-07-23T11:35:27.972\+00:00
- Summary: Most static matches are benign workflow syntax, documentation markup, fixed relative paths, or safe argument-list subprocess calls. Confirmed risks include eval-based command injection, unverified executable downloads, and predictable shared temporary directories. No prompt injection, credential collection, or data-exfiltration intent was found. Static review was capped at 400/549 representative findings; omitted static matches are unconfirmed, so automatic publishing stays disabled until manual review.

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- Downloads: 12
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