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Generate a FastQC quality report for raw reads

Run FastQC on raw FASTQ reads to produce an HTML quality report, then optionally merge many reports into one summary with MultiQC.

SSSudipta SardarUpdated July 21, 2026

Prerequisites

  • FastQC installed and on your PATH (requires a Java runtime, JDK 8 or newer)
  • One or more FASTQ files, plain (.fastq) or gzip-compressed (.fastq.gz)
  • MultiQC installed if you plan to aggregate reports (optional)

1Run FastQC into an output directory

Point FastQC at a FASTQ file and send the results to a dedicated output folder with -o (create it first with `mkdir -p qc/` if it does not exist). FastQC also accepts several files at once, e.g. `fastqc *.fastq.gz -o qc/`, to process a whole batch in one call.

bash
fastqc reads.fastq.gz -o qc/

Expected output

Started analysis of reads.fastq.gz
Approx 5% complete for reads.fastq.gz
Approx 10% complete for reads.fastq.gz
Approx 15% complete for reads.fastq.gz
Approx 20% complete for reads.fastq.gz
...
Approx 90% complete for reads.fastq.gz
Approx 95% complete for reads.fastq.gz
Approx 100% complete for reads.fastq.gz
Analysis complete for reads.fastq.gz

2Read the report and aggregate with MultiQC (optional)

FastQC writes qc/reads_fastqc.html (open it in a browser) alongside qc/reads_fastqc.zip. When you have many reports, MultiQC scans the directory of *_fastqc.zip files and merges them into a single interactive HTML summary.

bash
multiqc qc/ -o multiqc_report

Expected output


  /// MultiQC 🔍 | v1.21

       file_search | Search path : qc
         searching | ⏳ 100% Searching 2 files
            fastqc | Found 1 reports
     write_results | Data        : multiqc_report/multiqc_data
     write_results | Report      : multiqc_report/multiqc_report.html
           multiqc | MultiQC complete

Troubleshooting

Skipping 'reads.fastq.gz' which didn't exist, or couldn't be read

The path is wrong or the file is not readable. Confirm the filename and directory (ls reads.fastq.gz) and check file permissions.

Exception in thread "main" java.lang.UnsupportedClassVersionError (or FastQC won't start at all)

Java is missing or too old. Install a JDK, for example: conda install -c bioconda fastqc openjdk

References