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

# fastq\_quality\_trimmer(1)

Filters sequences based on quality

## NAME

fastq\_quality\_trimmer - Filters sequences based on quality

## DESCRIPTION

usage: fastq\_quality\_trimmer \[-h\] \[-v\] \[-t N\] \[-l N\] \[-z\] \[-i INFILE\] \[-o OUTFILE\] Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gordon@cshl.edu)

- \[-h\]

  \= This helpful help screen.

- \[-t N\]

  \= Quality threshold - nucleotides with lower

-

  quality will be trimmed (from the end of the sequence).

- \[-l N\]

  \= Minimum length - sequences shorter than this (after trimming)

-

  will be discarded. Default = 0 = no minimum length.

- \[-z\]

  \= Compress output with GZIP.

- \[-i INFILE\]

  \= FASTQ input file. default is STDIN.

-

  \[-o OUTFILE\] = FASTQ output file. default is STDOUT. \[-v\]         = 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.

## 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.