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.
npx skills add majiayu000/claude-skill-registry --skill assembly-qc --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Assembly QC Evaluate genome assembly quality with contiguity metrics (QUAST) and gene completeness (BUSCO). ## 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 quast.py assembly.fasta -r reference.fasta -o quast_output ``` ### Compare Multiple Assemblies ```bash quast.py assembly1.fa assembly2.fa assembly3.fa -o comparison ``` ### Key Options | Option | Description | |--------|-------------| | `-o` | Output directory | | `-r` | Reference genome | | `-g` | Gene annotations (GFF) | | `-t` | Threads | | `-m` | Min contig length (default: 500) | | `--large` | For large genomes (>100Mb) | | `--fragmented` | For highly fragmented assemblies | | `--scaffolds` | Input is scaffolds (includes N-gaps) | ### With Gene Annotations ```bash quast.py assembly.fasta -r reference.fasta -g genes.gff -o quast_output ``` ### For Large Geno
- Key Metrics
- QUAST
- Installation
- Basic Usage
- With Reference Genome
- Compare Multiple Assemblies
- Key Options
- With Gene Annotations
- For Large Genomes
- Output Files
- Key Output Metrics
- BUSCO
- List Available Lineages
- Common Lineages
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
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 majiayu000/claude-skill-registry --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 majiayu000/claude-skill-registry, a repository with 534 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.