How do I install the Bio Reporting Automated Qc Reports skill?

Run npx skillmds@latest add freedomintelligence/bio-reporting-automated-qc-reports in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Bio Reporting Automated Qc Reports skill do?

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Is Bio Reporting Automated Qc Reports free to use?

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Who published Bio Reporting Automated Qc Reports?

FreedomIntelligence (@freedomintelligence) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bio Reporting Automated Qc Reports by freedomintelligence

Name: Bio Reporting Automated Qc Reports
Author: FreedomIntelligence

File contents

name: bio-reporting-automated-qc-reports description: 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. tool_type: cli primary_tool: multiqc measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command

Automated QC Reports with MultiQC

Basic Usage

# 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 QC	FastQC, fastp, Cutadapt
Alignment	STAR, HISAT2, BWA, Bowtie2
Quantification	featureCounts, Salmon, kallisto
Variant Calling	bcftools, GATK
Single-cell	CellRanger, STARsolo

Configuration

Create multiqc_config.yaml:

title: "RNA-seq QC Report"
subtitle: "Project XYZ"
intro_text: "QC metrics for all samples"

# Custom sample name cleaning
extra_fn_clean_exts:
  - '.sorted'
  - '.dedup'

# Report sections to include
module_order:
  - fastqc
  - star
  - featurecounts

# Highlight samples
table_cond_formatting_rules:
  pct_mapped:
    fail: [{lt: 50}]
    warn: [{lt: 70}]

Custom Data

# Add custom data file
# File format: sample\tmetric1\tmetric2
multiqc results/ --data-format tsv --custom-data-file custom_metrics.tsv

Python API

from multiqc import run as multiqc_run

# Run programmatically
multiqc_run(analysis_dir='results/', outdir='qc_report/')

Related Skills

read-qc/quality-reports - Generate input FastQC reports
read-qc/fastp-workflow - Preprocessing QC
workflows/rnaseq-to-de - Full workflow with QC

---name: bio-reporting-automated-qc-reportsdescription: ---name: bio-reporting-automated-qc-reportsdescription: 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.tool_type: cliprimary_tool: multiqcmeasurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.allowed-tools: - read_file - run_shell_command---# Automated QC Reports with MultiQC## Basic Usage```bash# Aggregate all QC outputs in directorymultiqc results/ -o qc_report/# Specify output namemultiqc results/ -n my_project_qc# Include specific tools onlymultiqc results/ --module fastqc --module star```## Supported ToolsMultiQC recognizes outputs from 100+ bioinformatics tools:| Category | Tools ||----------|-------|| Read QC | FastQC, fastp, Cutadapt || Alignment | STAR, HISAT2, BWA, Bowtie2 || Quantification | featureCounts, Salmon, kallisto || Variant Calling | bcftools, GATK || Single-cell | CellRanger, STARsolo |## ConfigurationCreate `multiqc_config.yaml`:```yamltitle: "RNA-seq QC Report"subtitle: "Project XYZ"intro_text: "QC metrics for all samples"# Custom sample name cleaningextra_fn_clean_exts: - '.sorted' - '.dedup'# Report sections to includemodule_order: - fastqc - star - featurecounts# Highlight samplestable_cond_formatting_rules: pct_mapped: fail: [{lt: 50}] warn: [{lt: 70}]```## Custom Data```bash# Add custom data file# File format: sample\tmetric1\tmetric2multiqc results/ --data-format tsv --custom-data-file custom_metrics.tsv```## Python API```pythonfrom multiqc import run as multiqc_run# Run programmaticallymultiqc_run(analysis_dir='results/', outdir='qc_report/')```## Related Skills- read-qc/quality-reports - Generate input FastQC reports- read-qc/fastp-workflow - Preprocessing QC- workflows/rnaseq-to-de - Full workflow with QC

Frequently asked questions

Bio Reporting Automated Qc Reports