---
name: "fastx_clipper"
section: "1"
platform: "linux"
package: "fastx-toolkit"
version: "0.0.14-6"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/fastx_clipper"
---

# fastx\_clipper(1)

FASTA/Q Clipper

## NAME

fastx\_clipper - FASTA/Q Clipper

## DESCRIPTION

usage: fastx\_clipper \[-h\] \[-a ADAPTER\] \[-D\] \[-l N\] \[-n\] \[-d N\] \[-c\] \[-C\] \[-o\] \[-v\] \[-z\] \[-i INFILE\] \[-o OUTFILE\] Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)

- \[-h\]

  \= This helpful help screen.

-

  \[-a ADAPTER\] = ADAPTER string. default is CCTTAAGG (dummy adapter). \[-l N\]       = discard sequences shorter than N nucleotides. default is 5. \[-d N\]       = Keep the adapter and N bases after it.

-

  (using '-d 0' is the same as not using '-d' at all. which is the default).

- \[-c\]

  \= Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).

- \[-C\]

  \= Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).

- \[-k\]

  \= Report Adapter-Only sequences.

- \[-n\]

  \= keep sequences with unknown (N) nucleotides. default is to discard such sequences.

- \[-v\]

  \= Verbose - report number of sequences.

- If \[-o\] is specified,

  report will be printed to STDOUT.

-

  If \[-o\] is not specified (and output goes to STDOUT), report will be printed to STDERR.

- \[-z\]

  \= Compress output with GZIP.

- \[-D\]

  \= DEBUG output.

- \[-M N\]

  \= require minimum adapter alignment length of N.

- If less than N nucleotides aligned with the adapter - don't clip it.

  \[-i INFILE\]  = FASTA/Q input file. default is STDIN.

-

  \[-o OUTFILE\] = FASTA/Q output file. default is STDOUT.

## SEE ALSO

The quality of this automatically generated manpage might be insufficient.  It is suggested to visit

-

  http://hannonlab.cshl.edu/fastx\_toolkit/commandline.html

to get a better layout as well as an overview about connected FASTX tools.