---
title: "fastp"
description: "fastp is an all-in-one FASTQ pre-processing tool. It performs adapter trimming, quality filtering, per-read quality correction, and QC report generation in a single pass — typically faster than any…"
source: https://liatir.com/tools/fastp
---

# fastp

fastp is an all-in-one FASTQ pre-processing tool. It performs adapter trimming, quality filtering, per-read quality correction, and QC report generation in a single pass — typically faster than any pipeline that chains separate tools.

## Details

| Property | Value |
|----------|-------|
| Type | Native tool |
| Binary | `fastp` |

## Installation

Nothing to install. This tool ships inside Liatir and runs at the version this
release was tested with; it updates when Liatir updates. The tool page shows
**Included with Liatir** and the version it is running.

On Windows it runs through WSL2 — see
[Windows and WSL2](https://liatir.com/tools/overview#windows-and-wsl2).

## Accepted inputs

| Field | Extension(s) | Required |
|-------|-------------|---------|
| R1 (read 1) | `.fastq`, `.fastq.gz`, `.fq`, `.fq.gz` | Yes |
| R2 (read 2) | `.fastq`, `.fastq.gz`, `.fq`, `.fq.gz` | No (paired-end only) |

Providing only R1 runs fastp in **single-end** mode. Providing both R1 and R2 activates **paired-end** mode automatically. Paired-end mode enables additional QC checks (overlap analysis, insert size estimation) and correct adapter detection without needing to specify adapter sequences.

## Running fastp

1. Navigate to **Tools → fastp**.
2. Select an R1 file from your Data library.
3. Optionally select an R2 file for paired-end mode.
4. Click **Run**.

Liatir runs fastp with auto-detected adapter trimming and shows the trimmed output files in the results panel.

## Output files

fastp produces trimmed FASTQ files:

- **Single-end**: one trimmed R1 file named `fastp-<run-id>-R1.fastq.gz`
- **Paired-end**: trimmed R1 and R2 files

Each output file appears in the results panel above the QC stats, with two actions:

- **Add to Data** — registers the trimmed file in the Data library immediately. The file is available in any subsequent tool's file picker (e.g., as input to an aligner such as BWA-MEM or Minimap2) without any manual import step.
- **Save as…** — opens the system save dialog to copy the file to a location you choose.

::: tip After trimming
In a typical short-read DNA sequencing pipeline, trimmed reads from fastp feed directly into an aligner such as BWA-MEM or Minimap2. With Liatir's pipeline system, the trimmed files can be automatically wired to the aligner step's input.
:::

## QC statistics

fastp reports detailed statistics before and after filtering:

### Read counts

| Metric | Description |
|--------|-------------|
| Total reads (before) | Total reads input to fastp |
| Total bases (before) | Total base count before filtering |
| Total reads (after) | Reads remaining after all filters |
| Total bases (after) | Base count after filtering |

### Quality rates

| Metric | Description |
|--------|-------------|
| Q20 rate (before/after) | Fraction of bases with Phred quality ≥ 20 (error rate < 1%) |
| Q30 rate (before/after) | Fraction of bases with Phred quality ≥ 30 (error rate < 0.1%) |
| GC content | Overall GC percentage |

### Filter results

| Category | Description |
|----------|-------------|
| Passed filter | Reads retained after all filters |
| Low quality | Reads with too many bases below the quality threshold |
| Too many N | Reads exceeding the maximum allowed ambiguous bases |
| Too short | Reads shorter than the minimum length cutoff after trimming |

::: tip Interpreting Q30 rate
A Q30 rate above 80% after filtering is generally considered good for modern short-read Illumina data. Q30 rates below 70% may indicate run quality issues at the sequencing level.

Compare Q30 before and after to assess how much low-quality data was present. A large gain in Q30 from filtering means the raw data had significant noise at 3′ ends.
:::

## What fastp does automatically

By default, Liatir runs fastp with:

- **Auto adapter detection** — fastp detects adapter sequences from the data without needing adapter sequences specified. For paired-end data it uses read overlap; for single-end it uses built-in adapter profiles.
- **Per-read quality trimming** — trims low-quality bases from 3′ ends.
- **Minimum length filtering** — discards reads shorter than 15 bp after trimming.
- **Gzip-compressed output** — trimmed files are always written as `.fastq.gz`.