.TH YARA_INDEXER 1 "" "yara_indexer 0.9.10 [tarball]" ""
.SH NAME
yara_indexer \- Yara Indexer
.SH SYNOPSIS
\fByara_indexer\fP [\fIOPTIONS\fP] <\fIREFERENCE FILE\fP>
.SH DESCRIPTION
Yara - Yet Another Read Aligner.
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See \fIhttp://www.seqan.de/projects/yara\fP for more information.
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(c) Copyright 2011-2014 by Enrico Siragusa.
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(c) Copyright 2013 by NVIDIA Corporation.
.SH REQUIRED ARGUMENTS
.TP
\fBREFERENCE_FILE\fP \fIINPUT_FILE\fP
A reference genome file. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
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\fB--version\fP
Display version information.
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\fB-v\fP, \fB--verbose\fP
Displays verbose output.
.SS Output Options:
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\fB-o\fP, \fB--output-prefix\fP \fIOUTPUT_PREFIX\fP
Specify a filename prefix for the reference genome index.                                      Default: use the filename prefix of the reference genome.
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\fB-td\fP, \fB--tmp-dir\fP \fISTRING\fP
Specify a temporary directory where to construct the index.                                      Default: use the output directory.