---
name: "fastaq-chunker"
section: "1"
platform: "linux"
package: "fastaq"
version: "3.17.0-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastaq-chunker"
---

# fastaq-chunker(1)

Splits sequences into equal sized chunks

## NAME

fastaq\_chunker - Splits sequences into equal sized chunks

## DESCRIPTION

usage: fastaq\_chunker \[options\] \<infile\> \<out\> \<chunk size\> \<tolerance\>

Splits a multi sequence file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk\_size chunks in each file, but allows a little extra, so chunk can be up to (chunk\_size + tolerance), to prevent tiny chunks made from the ends of sequences

### positional arguments:

- infile

  Name of input file to be split

- out

  Prefix of output file. If **--onefile** used, then name of single output file

- chunk\_size

  Size of each chunk

- tolerance

  Tolerance allowed in chunk size

### options:

- **-h**, **--help**

  show this help message and exit

- **--onefile**

  Output all the sequences in one file

- **--skip\_all\_Ns**

  Do not output any sequence that consists of all Ns