community/fastq-qc
WASM NewBrowser-based FASTQ quality control reports. Generate per-base quality, adapter content, and GC distribution plots client-side.
Overview
FASTQ QC generates FastQC-style quality reports entirely in your browser. Drop a FASTQ file (plain or gzipped) and get per-base quality distributions, GC content curves, adapter contamination checks, and sequence length histograms — all computed client-side with WebAssembly.
Features
- Per-base quality — Box-and-whisker plots of Phred scores at each read position.
- Quality score distribution — Histogram of mean quality scores across all reads.
- GC content — Per-sequence GC distribution compared to a theoretical normal.
- Sequence length — Distribution of read lengths for variable-length datasets.
- Adapter content — Detection of common adapter sequences (Illumina, Nextera, SOLiD).
- Duplication levels — Estimate of library complexity from sequence duplication rates.
- Overrepresented sequences — Flag sequences appearing more often than expected.
How It Works
The tool streams FASTQ records through cyanea-io’s parser in a Web Worker. cyanea-seq handles base encoding and adapter matching, while cyanea-stats computes the statistical summaries. Results are plotted with a lightweight charting library. Processing speed is typically 1-2 million reads per second.
Use Cases
- Pre-alignment QC — Check read quality before running an alignment pipeline.
- Sequencing core reports — Generate QC summaries without server infrastructure.
- Troubleshooting — Diagnose adapter contamination or quality drop-off at read ends.
- Teaching — Show students what good and bad sequencing data looks like interactively.