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

# fastaq-trim\_contigs(1)

Trims a set number of bases off the end of every contig

## NAME

fastaq\_trim\_contigs - Trims a set number of bases off the end of every contig

## DESCRIPTION

usage: fastaq\_trim\_contigs \[options\] \<infile\> \<outfile\>

Trims a set number of bases off the end of every contig, so gaps get bigger and contig ends are removed. Bases are replaced with Ns. Any sequence that ends up as all Ns is lost

### positional arguments:

- infile

  Name of input file

- outfile

  Name of output file

### options:

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

  show this help message and exit

- **--trim\_number** TRIM\_NUMBER

  Number of bases to trim around each gap, and off ends of each sequence \[100\]