---
name: "optimir"
section: "1"
platform: "linux"
package: "optimir"
version: "1.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/optimir"
---

# optimir(1)

Integrating genetic variations in miRNA alignment

## NAME

optimir - Integrating genetic variations in miRNA alignment

## SYNOPSIS

**optimir** \[*options*\]

## DESCRIPTION

OptimiR is a miRSeq data alignment workflow. It integrates genetic information to assess the impact of variants on miRNA expression. OptimiR: A bioinformatics pipeline designed to detect and quantify miRNAs, isomiRs and polymiRs from miRSeq data, and study the impact of genetic variations on polymiRs' expression.

## OPTIONS

### Basic options

- **-h, --help**

  Produce help message

### Subcommands

- **process**

  Process a single fastq file with the OptimiR workflow

- **summarize**

  Summarize results of previously processed samples

- **libprep**

  Only prepare small RNA alignment library sequences that integrates genetic variants (required before processing multiple samples in parallel)

## SEE ALSO

**https://github.com/FlorianThibord/OptimiR**

## AUTHOR

OptimiR was written by Florian Thibord.