Genomics Assembly

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---
name: bio-genomics-assembly
description: 'Genome assembly quality assessment: N50/N90/L50/L90 (QUAST-compatible),
  GC content, contig length distribution, completeness estimation. Wraps SPAdes, Megahit,
  Flye, Canu.'
tool_type: mixed
primary_tool: genomics
measurable_outcome: Execute skill workflow successfully with valid output within 15
  minutes.
allowed-tools:
- read_file
- run_shell_command
---

# 🧬 Genome Assembly

De novo genome assembly for short and long reads. Wraps SPAdes, Megahit, Flye, and Canu.

## CLI Reference

```bash
python omicsclaw.py run genomics-assembly --demo
python omicsclaw.py run genomics-assembly --input <reads.fastq> --output <dir>
```

## Why This Exists

- **Without it**: Assemblies require intense memory management and parameter orchestration per graph build
- **With it**: Automated contig building and K-mer tuning logic across read modalities
- **Why OmicsClaw**: Unified containerized or local graph assembler invocation

## Workflow

1. **Calculate**: Prepare k-mer frequencies or long-read overlaps.
2. **Execute**: Build de Bruijn or string graphs.
3. **Assess**: Perform contig polishing and scaffolding.
4. **Generate**: Output structural FASTA representations.
5. **Report**: Synthesize N50 stats and completeness metrics.

## Example Queries

- "Assemble my isolate using SPAdes"
- "De novo genome assembly using Flye"

## Output Structure

```
output_directory/
├── report.md
├── result.json
├── assembled.fa
├── figures/
│   └── assembly_graph.png
├── tables/
│   └── quast_metrics.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256
```

## Safety

- **Local-first**: Strict offline processing without external upload.
- **Disclaimer**: Requires OmicsClaw reporting structures and disclaimers.
- **Audit trail**: Hyperparameters and operational flow states are logged fully.

## Integration with Orchestrator

**Trigger conditions**:
- Automatically invoked dynamically based on tool metadata and user intent matching.

**Chaining partners**:
- `genomics-qc` — Upstream read trimming
- `annotation` — Downstream genome annotation

## Citations

- [SPAdes](https://doi.org/10.1089/cmb.2012.0021)
- [Flye](https://doi.org/10.1038/s41587-019-0072-8)

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