---
name: "nxtrim"
section: "1"
platform: "linux"
package: "nxtrim"
version: "0.4.3+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/nxtrim"
---

# nxtrim(1)

\<short\_description\>

## NAME

nxtrim - \<short\_description\>

## SYNOPSIS

**nxtrim** *-1 R1.fastq.gz -2 R2.fastq.gz* \[*options*\]

## DESCRIPTION

Program:        nxtrim Version:        v0.4.3 Contact:        joconnell@illumina.com

## COPYRIGHT

Copyright © 2016, Illumina, Inc. All rights reserved. See LICENSE for further details.

### Required arguments:

- **-1** \[ **--r1** \] arg

  read 1 in fastq format (gzip allowed)

- **-2** \[ **--r2** \] arg

  read 2 in fastq format (gzip allowed)

### Allowed options:

- **-O** \[ **--output-prefix** \] arg

  output prefix

- **--justmp**

  just creates a the mp/unknown libraries (reads with adapter at the start will be completely N masked)

- **--stdout**

  print trimmed reads to stdout (equivalent to justmp)

- **--stdout-mp**

  print only known MP reads to stdout (good for scaffolding)

- **--stdout-un**

  print only unknown reads to stdout

- **--rf**

  leave mate pair reads in RF orientation \[by default are flipped into FR\]

- **--preserve-mp**

  preserve MPs even when the corresponding PE has longer reads

- **--ignorePF**

  ignore chastity/purity filters in read headers

- **--separate**

  output paired reads in separate files (prefix\_R1/prefix\_r2). Default is interleaved.

- **-a**, **--aggressive**

  more aggressive adapter search (see docs/adapter.md)

- **-s**, **--similarity** arg (=0.85)

  The minimum similarity between strings to be considered a match (Hamming distance divided by string length)

- **-v**, **--minoverlap** arg (=12)

  The minimum overlap to be considered for matching

- **-l**, **--minlength** arg

  (=21)      The minimum read length to output (smaller reads will be filtered)

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.