---
name: "fix-trinity-output"
section: "1"
platform: "linux"
package: "ruby-fix-trinity-output"
version: "1.0.0-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fix-trinity-output"
---

# fix-trinity-output(1)

Fix output fastq files from Trinity

## NAME

fix-trinity-output - Fix output fastq files from Trinity

## DESCRIPTION

Trinity outputs fastq files that have been 'corrected'

Unfortunately these files are no longer properly paired and therefore can't be used in most aligners such as bowtie2 and snap

This script attempts to fix that and produce 2 properly paired fastq files and a fastq file containing single reads

## OPTIONS

- **--left**, **-l** \<s\>:

  fastq file of left reads

- **--right**, **-r** \<s\>:

  fastq file of right reads

- **--output**, **-o** \<s\>:

  output prefix

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

  Show this message