🧬 Genome Assembly

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

CLI Reference

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
• Flye