fastqc ☆

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Description:
Quality control tool for high throughput sequence data

Type: Formula | Latest Version: 0.12.1@0 | Tracked Since: Dec 17, 2025

Links: Homepage | formulae.brew.sh

Category: Other

Tags: bioinformatics sequencing quality-control ngs genomics

Install: brew install fastqc

About:
FastQC is a Java-based application that performs quality control checks on raw sequence data from high-throughput sequencing pipelines. It provides a modular set of analysis modules to assess the quality of reads, including per-base quality scores, adapter content, and sequence duplication levels. The tool generates interactive HTML reports, enabling researchers to identify potential issues and verify the technical quality of their data before downstream analysis.

Key Features:

Generates comprehensive HTML reports with graphs and statistics
Detects adapter contamination and overrepresented sequences
Analyzes per-base quality scores, GC content, and sequence duplication
Platform-independent Java application with a simple graphical interface

Use Cases:

Validating raw read quality from Illumina sequencing runs
Identifying adapter sequences or technical artifacts in NGS data
Generating QC reports for pre-processing pipeline inputs

Alternatives:

Fastp – Fastp is an all-in-one tool that performs both QC and trimming, often faster and suitable for automated pipelines, whereas FastQC is primarily for reporting.
MultiQC – MultiQC aggregates results from multiple tools, including FastQC, into a single report; it complements FastQC rather than replacing it.

License: GPL-3.0-or-later

Dependencies: openjdk

Bottles available for: all

Version History

Detected	Version	Rev	Change	Commit