yara_indexer

Yara Indexer

Provided by: seqan-apps (Version: 2.4.0+dfsg-14ubuntu1)
Source: seqan2
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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.