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claude-codescience

Claude-skill-registry bio-assembly-qc

Assemble genomes/metagenomes and produce assembly QC artifacts.

install
source · Clone the upstream repo
git clone https://github.com/majiayu000/claude-skill-registry
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/bio-assembly-qc" ~/.claude/skills/majiayu000-claude-skill-registry-bio-assembly-qc && rm -rf "$T"
manifest: skills/data/bio-assembly-qc/SKILL.md
tags
#genome-assembly#metagenome-assembly#quast-analysis#assembly-qc#spades#flye
source content

Bio Assembly QC

When to use

  • Assemble genomes/metagenomes and produce assembly QC artifacts.

Prerequisites

  • Tools installed via pixi (see pixi.toml).
  • Sufficient disk and RAM for chosen assembler.

Inputs

  • reads/*.fastq.gz (raw reads).
  • assembler choice (spades | flye).

Outputs

  • results/bio-assembly-qc/contigs.fasta
  • results/bio-assembly-qc/assembly_metrics.tsv
  • results/bio-assembly-qc/qc_report.html
  • results/bio-assembly-qc/logs/

Steps

  1. Select assembler based on read type and genome size.
  2. Run assembly with resource-aware settings.
  3. Run QUAST/MetaQUAST and summarize metrics.

QC gates

  • Assembly size range and N50 distribution meet project thresholds.
  • On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.

Validation

  • Verify reads are present and gzip-readable.
  • Check available disk space before assembly.

Tools

  • spades v4.2.0
  • flye v2.9.6
  • quast v5.3.0

Paper summaries (2023-2025)

  • summaries/ (include example use cases and tool settings used)

Tool documentation

  • SPAdes - De novo genome/metagenome assembler
  • Flye - Long-read assembly for PacBio and Nanopore
  • QUAST - Assembly quality assessment and metrics

References

  • See ../bio-skills-references.md