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genomics-assembly

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Load when computing genome-assembly QC metrics — N50/N90, L50/L90, total length, contig count, GC content, longest-contig — from a FASTA produced by any assembler (SPAdes / Megahit / Flye / Canu). Skip when running the assembly itself or when assessing alignment quality (use `genomics-alignment`).

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How to use this skill

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Source SKILL.md: https://github.com/TianGzlab/OmicsClaw/blob/HEAD/skills/genomics/genomics-assembly/SKILL.md

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genomics-assembly

When to use

The user has a FASTA from any de novo assembler (SPAdes, Megahit, Flye, Canu, etc.) and wants standard QUAST-compatible quality metrics: contig count, N50 / N90, L50 / L90, total length, longest contig, GC content, optional completeness fraction (when --genome-size is provided).

This skill does NOT run the assembly. It consumes the FASTA the assembler emits.

Inputs & Outputs

InputFormatRequired
Assembled contigs.fasta / .fayes (unless --demo)
Expected genome size--genome-size <bp> (used for completeness %)optional
OutputPathNotes
Per-contig tabletables/contig_lengths.csvone row per contig with contig + length (no GC column — GC is assembly-wide only)
Assembly metricstables/assembly_metrics.csvone-row N50/L50/total/longest summary
Reportreport.md + result.jsonalways

Flow

  1. Load FASTA (--input <assembly.fasta>) or generate a demo assembly at output_dir/demo_assembly.fasta (genome_assembly.py:186).
  2. Parse contigs (genome_assembly.py:52-67); each line is uppercased on read so case is normalised.
  3. Sort by length; compute cumulative N50 / N90 / L50 / L90 + total / longest + assembly-wide GC% from concatenated sequence.
  4. If --genome-size is set and > 0, compute completeness_pct = total_length / genome_size * 100.
  5. Write tables/contig_lengths.csv (genome_assembly.py:309) + tables/assembly_metrics.csv (:312) + report.md + result.json.

Gotchas

  • No assembler is invoked. This skill summarises an existing FASTA — it does not run SPAdes / Megahit / Flye / Canu. Run them upstream and feed the resulting FASTA here.
  • --input REQUIRED unless --demo. genome_assembly.py:290 raises ValueError("--input required when not using --demo"); non-existent paths raise FileNotFoundError at :293.
  • --genome-size 0 (default) skips completeness. Without an expected genome size (genome_assembly.py:279, default 0), the report omits the completeness column entirely. Pass --genome-size 3000000000 for a human-scale assembly to populate it.
  • Soft-masked bases are normalised to uppercase before GC counting. genome_assembly.py:67 calls line.upper() per FASTA line, so lowercase soft-masked regions contribute identically to hard-masked / unmasked sequence in the GC%. There is no way to exclude soft-masked regions short of pre-filtering the FASTA.
  • Demo FASTA has 100 contigs of varying length. --demo writes a fixed-pattern synthetic file useful for orchestrator smoke tests; the N50 it produces is not biologically meaningful.

Key CLI

# Demo
python omicsclaw.py run genomics-assembly --demo --output /tmp/asm_demo

# Real assembly with completeness against expected size
python omicsclaw.py run genomics-assembly \
  --input my_assembly.fasta --output results/ \
  --genome-size 3100000000

See also

  • references/parameters.md — every CLI flag
  • references/methodology.md — N50 / L50 definitions, GC interpretation
  • references/output_contract.md — tables/assembly_metrics.csv schema
  • Adjacent skills: genomics-alignment (downstream — map reads back to your assembly to validate), genomics-qc (upstream — FASTQ QC before assembly), genomics-cnv-calling (parallel — copy-number on a known reference instead of de novo)