Quality Control + Read Trimming
FastQC, MultiQC, Trimmomatic, fastp — diagnose and clean raw reads.
What this module covers
- ▸FastQC: per-base quality, GC content, adapter contamination
- ▸MultiQC: aggregating reports across samples
- ▸Trimmomatic: adapter removal, quality sliding window
- ▸fastp: faster alternative, hands-on comparison
Start here — the data journey
live in your browser · no installWatch the data move through the pipeline below, then read on — each section has its own interactive explorer embedded right where the code builds that figure, so you can turn the knobs as you go.
The quality-control pipeline
Millions of reads with per-base quality that sags toward the 3′ end and some adapter read-through.
Per-base quality, GC content, and adapter-content modules flag what needs fixing — one report per sample.
Collapses dozens of FastQC reports into one view so you can spot the outlier sample at a glance.
Sliding-window quality trimming + adapter removal. Reads get shorter but cleaner; very short reads are dropped.
High-quality, adapter-free reads. Re-run FastQC to prove the cleanup worked — then hand off to Module 4.
The notebook — live & editable
runs in your browser · no installEvery section's code is already filled in below. Press the ▶ next to any cell (or Shift+Enter) to run it, edit it and run again, or hit Run all to execute the whole notebook top to bottom. No Python or Jupyter install needed — the kernel boots right here in your browser.