Preprocessing with fastp

fastp is a fast all-in-one FASTQ preprocessor that handles adapter trimming, quality filtering, and read pruning.

Running Preprocessing

1. Navigate to your project → Run tab → Preprocessing step
2. Configure parameters (or use defaults)
3. Select samples to process
4. Click Run

Parameters

Parameter	Default	Description
Quality threshold	20	Minimum base quality score
Minimum length	36	Discard reads shorter than this
Cut front/tail	Off	Sliding window trimming from ends
Window size	4	Sliding window size
Mean quality	20	Mean quality threshold for window
Trim poly-G	Off	Remove poly-G tails (NextSeq/NovaSeq)
Trim poly-X	Off	Remove poly-X tails
Custom adapters	Auto	Override auto-detected adapters

Output

After preprocessing, you’ll see per-sample statistics:

• Reads before/after — How many reads passed filtering
• Pass rate — Percentage of reads retained
• Q30 rate after — Quality improvement after trimming

Tips

• Start with defaults — they work well for most Illumina data
• Enable poly-G trimming for NextSeq or NovaSeq data
• Lower the quality threshold (e.g., 15) if too many reads are being discarded