| name | genomics-assembly |
| description | 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`). |
| version | 0.5.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["genomics","assembly","n50","l50","contig","quast","spades","flye"] |
| requires | ["pandas","numpy"] |
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
| Input | Format | Required |
|---|
| Assembled contigs | .fasta / .fa | yes (unless --demo) |
| Expected genome size | --genome-size <bp> (used for completeness %) | optional |
| Output | Path | Notes |
|---|
| Per-contig table | tables/contig_lengths.csv | one row per contig with contig + length (no GC column — GC is assembly-wide only) |
| Assembly metrics | tables/assembly_metrics.csv | one-row N50/L50/total/longest summary |
| Report | report.md + result.json | always |
Flow
- Load FASTA (
--input <assembly.fasta>) or generate a demo assembly at output_dir/demo_assembly.fasta (genome_assembly.py:186).
- Parse contigs (
genome_assembly.py:52-67); each line is uppercased on read so case is normalised.
- Sort by length; compute cumulative N50 / N90 / L50 / L90 + total / longest + assembly-wide GC% from concatenated sequence.
- If
--genome-size is set and > 0, compute completeness_pct = total_length / genome_size * 100.
- 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
python omicsclaw.py run genomics-assembly --demo --output /tmp/asm_demo
python omicsclaw.py run genomics-assembly \
--input my_assembly.fasta --output results/ \
--genome-size 3100000000
See also
references/parameters.md — every CLI flagreferences/methodology.md — N50 / L50 definitions, GC interpretationreferences/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)
