Agent skill · Code Review & Quality

bio-genome-assembly-assembly-qc

Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill assembly-qc --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 3
SKILL.md size: 9 KB
Bundled scripts: yes
Path: skills/bioskills/assembly-qc/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

## Version Compatibility Reference examples tested with: BUSCO 5.5+, QUAST 5.2+, SPAdes 3.15+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Assembly QC **"Assess my genome assembly quality"** → Evaluate assembly contiguity (N50, total length, misassemblies) and gene completeness using conserved single-copy orthologs. - CLI: `quast assembly.fa -r reference.fa` (contiguity), `busco -i assembly.fa -l lineage` (completeness) ## Key Metrics | Metric | Good Assembly | |--------|---------------| | N50 | High (relative to genome) | | L50 | Low | | Contigs | Few | | Misassemblies | 0 (with reference) | | BUSCO Complete | >95% | | BUSCO Duplicated | <5% (unless polyploid) | ## QUAST ### Installation ```bash conda install -c bioconda quast ``` ### Basic Usage ```bash quast.py assembly.fasta -o quast_output ``` ### With Reference Genome ```bash qu

What's inside
Steps it walks through
  1. Version Compatibility
  2. Key Metrics
  3. QUAST
  4. Installation
  5. Basic Usage
  6. With Reference Genome
  7. Compare Multiple Assemblies
  8. Key Options
  9. With Gene Annotations
  10. For Large Genomes
  11. Output Files
  12. Key Output Metrics
  13. BUSCO
  14. List Available Lineages
Ships with 2 files
  • examples/run_qc.sh
  • usage-guide.md
Commands it runs
conda install -c bioconda quast
quast.py assembly.fasta -o quast_output
quast.py assembly.fasta -r reference.fasta -o quast_output
quast.py assembly1.fa assembly2.fa assembly3.fa -o comparison
quast.py assembly.fasta -r reference.fasta -g genes.gff -o quast_output
quast.py --large assembly.fasta -o quast_output -t 16
conda install -c bioconda busco
busco -i assembly.fasta -m genome -l bacteria_odb10 -o busco_output
busco --list-datasets
busco -i assembly.fasta -m genome --auto-lineage -o busco_output
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About this skill
What does the bio-genome-assembly-assembly-qc skill do?

Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill assembly-qc --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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