fastp

name	fastp
description	Use when processing raw FASTQ files for quality control, adapter trimming, length or complexity filtering, polyG tail trimming, or generating QC reports before downstream analysis.
disable-model-invocation	true
user-invocable	true

fastp

Quick Start

• Command: fastp
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/fastp
• Version: 1.1.0
• Full options: see references/help.md

When To Use This Tool

• One-stop FASTQ preprocessing before alignment or quantification.
• Adapter trimming, quality filtering, polyG/polyX trimming, and QC reporting in one run.
• Best default choice when you want both cleaned FASTQ and an HTML/JSON report.
• Prefer cutadapt when trimming logic needs very explicit adapter semantics or more surgical control.

Common Patterns

# 1) Single-end QC + trimming
fastp \
  -i sample.fastq.gz \
  -o sample.clean.fastq.gz \
  -h sample.fastp.html \
  -j sample.fastp.json \
  -w 8

fastp \
  -i sample_R1.fastq.gz \
  -I sample_R2.fastq.gz \
  -o sample_R1.clean.fastq.gz \
  -O sample_R2.clean.fastq.gz \
  -h sample.fastp.html \
  -j sample.fastp.json \
  -w 8