bio-reporting-automated-qc-reports
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
npx skills add BioTender-max/awesome-bio-agent-skills --skill automated-qc-reports --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.
## Version Compatibility Reference examples tested with: Cell Ranger 8.0+, FastQC 0.12+, GATK 4.5+, HISAT2 2.2.1+, MultiQC 1.21+, STAR 2.7.11+, Subread 2.0+, bcftools 1.19+, fastp 0.23+, kallisto 0.50+ 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. # Automated QC Reports with MultiQC **"Aggregate QC results into one report"** → Combine outputs from FastQC, samtools, Picard, and other tools into a single interactive HTML report. - CLI: `multiqc .` (scans current directory for recognized tool outputs) ## Basic Usage ```bash # Aggregate all QC outputs in directory multiqc results/ -o qc_report/ # Specify output name multiqc results/ -n my_project_qc # Include specific tools only multiqc results/ --module fastqc --module star ``` ## Supported Tools MultiQC recognizes outputs from 100+ bioinformatics tools: | Category | Tools | |----------|-------| | Read
- Version Compatibility
- Basic Usage
- Supported Tools
- Configuration
- Custom Data
- Python API
- Related Skills
Aggregate all QC outputs in directory multiqc results/ -o qc_report/ Specify output name multiqc results/ -n my_project_qc Include specific tools only multiqc results/ --module fastqc --module star Add custom data file File format: sample\tmetric1\tmetric2 multiqc results/ --data-format tsv --custom-data-file custom_metrics.tsv
What does the bio-reporting-automated-qc-reports skill do?
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill automated-qc-reports --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.