---
name: "yara_indexer"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/yara_indexer"
---

# yara\_indexer(1)

Yara Indexer

## NAME

yara\_indexer - Yara Indexer

## SYNOPSIS

**yara\_indexer** \[*OPTIONS*\] \<*REFERENCE FILE*\>

## DESCRIPTION

Yara - Yet Another Read Aligner.

See *http://www.seqan.de/projects/yara* for more information.

(c) Copyright 2011-2014 by Enrico Siragusa.

(c) Copyright 2013 by NVIDIA Corporation.

## REQUIRED ARGUMENTS

- **REFERENCE\_FILE** *INPUT\_FILE*

  A reference genome file. Valid filetypes are: *.sam\[.\*\]*, *.raw\[.\*\]*, *.gbk\[.\*\]*, *.frn\[.\*\]*, *.fq\[.\*\]*, *.fna\[.\*\]*, *.ffn\[.\*\]*, *.fastq\[.\*\]*, *.fasta\[.\*\]*, *.faa\[.\*\]*, *.fa\[.\*\]*, *.embl\[.\*\]*, and *.bam*, where \* is any of the following extensions: *gz*, *bz2*, and *bgzf* for transparent (de)compression.

## OPTIONS

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

  Display the help message.

- **--version**

  Display version information.

- **-v**, **--verbose**

  Displays verbose output.

### Output Options:

- **-o**, **--output-prefix** *OUTPUT\_PREFIX*

  Specify a filename prefix for the reference genome index.                                      Default: use the filename prefix of the reference genome.

- **-td**, **--tmp-dir** *STRING*

  Specify a temporary directory where to construct the index.                                      Default: use the output directory.