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.