AgentSkillsCN

bio-reporting-automated-qc-reports

利用 MultiQC 汇总 FastQC、比对及其他工具的指标，生成标准化的质量控制报告。当您需要汇总各样本的 QC 指标，创建可共享的质量报告，或构建自动化的 QC 流程时，请使用此方法。

SKILL.md
--- frontmatter
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

Automated QC Reports with MultiQC

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:

CategoryTools
Read QCFastQC, fastp, Cutadapt
AlignmentSTAR, HISAT2, BWA, Bowtie2
QuantificationfeatureCounts, Salmon, kallisto
Variant Callingbcftools, GATK
Single-cellCellRanger, STARsolo

Configuration

Create multiqc_config.yaml:

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

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

Python API

python
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