---
name: "fastq-clipper"
section: "1"
platform: "linux"
package: "ea-utils"
version: "1.1.2+dfsg-9+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastq-clipper"
---

# fastq-clipper(1)

ea-utils: removes one or more adapter sequences from the fastq file

## NAME

fastq-clipper - ea-utils: removes one or more adapter sequences from the fastq file

## DESCRIPTION

usage: fastq-clipper \[options\] \<fastq-file\> \<adapters\>

Removes one or more adapter sequences from the fastq file. Adapter sequences are colon-delimited. Stats go to stderr, unless **-o** is specified.

## OPTIONS

- **-h**

  This help

- **-o** FIL

  Output file (stats to stdout)

- **-p** N

  Maximum difference percentage (10)

- **-m** N

  Minimum clip length (1)

- **-l** N

  Minimum remaining sequence length (15)

- **-x** \[N\]

  Extra match length past adapter length,

-

  N =-1 : search all N = 0 : search only up to adapter length

- **-e**

  End-of-line (default)

- **-b**

  Beginning-of-line (not supported yet)