Quality Reports

Quality Reports

Generate quality reports for FASTQ files using FastQC and aggregate multiple reports with MultiQC.

FastQC - Single Sample Reports

Basic Usage

# Single file
fastqc sample.fastq.gz

# Multiple files
fastqc *.fastq.gz

# Specify output directory
fastqc -o qc_reports/ sample_R1.fastq.gz sample_R2.fastq.gz

# Set threads
fastqc -t 4 *.fastq.gz

Output Files

FastQC produces two files per input:

• sample_fastqc.html - Interactive HTML report
• sample_fastqc.zip - Data files and images

Key Modules

Extract Data from ZIP

# Unzip to access raw data
unzip sample_fastqc.zip

# View summary
cat sample_fastqc/​summary.txt

# Get per-base quality
cat sample_fastqc/​fastqc_data.txt | grep -A 50 ">>Per base sequence quality"

MultiQC - Aggregate Reports

Basic Usage

# Aggregate all FastQC reports in current directory
multiqc .

# Specify input and output
multiqc qc_reports/ -o multiqc_output/

# Custom report name
multiqc . -n my_project_qc

# Force overwrite
multiqc . -f

Common Options

# Flat directory (no sample subdirs)
multiqc --flat .

# Export data as TSV
multiqc . --export

# Only specific modules
multiqc . -m fastqc

# Exclude patterns
multiqc . --ignore '*_trimmed*'

# Include patterns
multiqc . --ignore-samples '*negative*'

Output Files

• multiqc_report.html - Interactive HTML report
• multiqc_data/ - Directory with data tables
  • multiqc_fastqc.txt - FastQC metrics
  • multiqc_general_stats.txt - Summary statistics
  • multiqc_sources.txt - Source files used

Extract Data Programmatically

import pandas as pd

general_stats = pd.read_csv('multiqc_data/​multiqc_general_stats.txt', sep='\t')
print(general_stats.columns)

fastqc_data = pd.read_csv('multiqc_data/​multiqc_fastqc.txt', sep='\t')

Batch Processing

Process Multiple Samples

# All FASTQ files in parallel
fastqc -t 8 -o qc_reports/ raw_data/​*.fastq.gz

# Then aggregate
multiqc qc_reports/ -o multiqc_output/

Before and After Trimming

# Create separate directories
mkdir -p qc_reports/​raw qc_reports/​trimmed

# QC raw reads
fastqc -o qc_reports/​raw/ raw_data/​*.fastq.gz

# After trimming (using fastp, cutadapt, etc.)
fastqc -o qc_reports/​trimmed/ trimmed_data/​*.fastq.gz

# Compare with MultiQC
multiqc qc_reports/ -o qc_comparison/

Interpretation Guide

Quality Scores

Common Issues

Configuration

Custom Adapters

Create ~/​.fastqc/​Configuration/​adapter_list.txt:

Custom_Adapter_Name    ACGTACGTACGT

Custom Limits

Create ~/​.fastqc/​Configuration/​limits.txt to customize thresholds:

# Warn if mean quality below 25
quality_sequence    warn    25
quality_sequence    error   20

Related Skills

• adapter-trimming - Remove adapters detected by FastQC
• fastp-workflow - All-in-one QC and trimming
• sequence-io/​read-sequences - FASTQ file reading/​writing