FastQC

Generate sequencing read quality-control reports for FASTQ, BAM and SAM files

Supported formats: FASTQ, FASTQ.GZ, BAM and SAM (Maximum size: 500 MB)

FastQC

Function

FastQC is a widely used quality-control application for high-throughput sequencing data. It analyzes sequencing reads and generates graphical reports highlighting potential quality issues such as low-quality bases, adapter contamination, sequence duplication, GC bias, and overrepresented sequences.

Input Format

  • FASTQ files (.fastq, .fq)
  • Compressed FASTQ files (.fastq.gz, .fq.gz)
  • BAM files (.bam)
  • SAM files (.sam)
  • Single-end or paired-end sequencing data.

Output Format

  • Interactive HTML report.
  • ZIP archive containing all FastQC results.
  • Per-base quality plots.
  • GC-content statistics.
  • Adapter and duplication analyses.

Applications

  • Raw sequencing quality assessment.
  • Detecting adapter contamination.
  • Identifying low-quality sequencing runs.
  • Comparing quality across samples.
  • Preparing data for trimming and filtering.

Example Usage

fastqc input.fastq.gz \
-o fastqc_output/

fastqc *.fastq.gz \
-o fastqc_output/ \
-t 8

fastqc aligned.bam \
-o fastqc_output/

multiqc fastqc_output/ \
-o multiqc_report/

Suggested Reading

Citation

Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data . Babraham Bioinformatics, 2010.
Important Notes:
  • Pass, warning and fail flags should be interpreted in the context of the sequencing experiment.
  • Some FastQC warnings are expected for RNA-seq, amplicon sequencing, bisulfite sequencing and targeted assays.
  • Adapter contamination should generally be removed before downstream analysis.
  • Paired-end files are analyzed independently and should be reviewed together.
  • FastQC is typically the first step before trimming, alignment, assembly or variant calling.