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.