.TH YARA_MAPPER 1 "" "yara_mapper 0.9.10 [tarball]" ""
.SH NAME
yara_mapper \- Yara Mapper
.SH SYNOPSIS
\fByara_mapper\fP [\fIOPTIONS\fP] <\fIREFERENCE INDEX PREFIX\fP> <\fISE-READS FILE\fP>
.br
\fByara_mapper\fP [\fIOPTIONS\fP] <\fIREFERENCE INDEX PREFIX\fP> <\fIPE-READS FILE 1\fP> <\fIPE-READS FILE 2\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_INDEX_PREFIX\fP \fIINPUT_PREFIX\fP
An indexed reference genome.
.TP
\fBREADS_FILE\fP List of \fIINPUT_FILE\fP's
Either one single-end or two paired-end / mate-pair read files. 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 global statistics.
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\fB-vv\fP, \fB--very-verbose\fP
Displays extensive statistics for each batch of reads.
.SS Output Options:
.TP
\fB-o\fP, \fB--output-file\fP \fIOUTPUT_FILE\fP
Specify an output file. Default: write the file to standard output. Valid filetypes are: \fI.sam[.*]\fP and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fB-f\fP, \fB--output-format\fP \fISTRING\fP
Specify an output format. Note: when specifying the option                                                             --output-file, the output format is taken from the filename                                                             extension. One of \fIbam\fP, \fIsam\fP, \fIsam.bgzf\fP, \fIsam.gz\fP, and \fIsam.bz2\fP. Default: \fIsam\fP.
.TP
\fB-rg\fP, \fB--read-group\fP \fISTRING\fP
Specify a read group for all records in the SAM/BAM file. Default: \fInone\fP.
.TP
\fB-sa\fP, \fB--secondary-alignments\fP \fISTRING\fP
Specify whether to output secondary alignments in                                                                     the XA tag of the primary alignment, as separate                                                                     secondary records, or to omit them. One of \fItag\fP, \fIrecord\fP, and \fIomit\fP. Default: \fItag\fP.
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\fB-ra\fP, \fB--rabema-alignments\fP
Output alignments compatible with the                                                                  Read Alignment BEnchMArk (RABEMA).
.SS Mapping Options:
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\fB-e\fP, \fB--error-rate\fP \fIINTEGER\fP
Consider alignments within this percentual number of errors.                                          Increase this threshold to increase the number of mapped reads.                                          Decrease this threshold to decrease the runtime. In range [0..10]. Default: \fI5\fP.
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\fB-s\fP, \fB--strata-rate\fP \fIINTEGER\fP
Consider suboptimal alignments within this percentual number                                       of errors from the optimal alignment. Increase this threshold to increase                                       the number of alternative alignments at the expense of runtime. In range [0..10]. Default: \fI0\fP.
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\fB-y\fP, \fB--sensitivity\fP \fISTRING\fP
Sensitivity with respect to edit distance.                                                           Full sensitivity guarantees to find all considered alignments                                                           but increases runtime, low sensitivity decreases runtime by                                                           breaking such guarantee. One of \fIlow\fP, \fIhigh\fP, and \fIfull\fP. Default: \fIhigh\fP.
.SS Paired-End Mapping Options:
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\fB-ll\fP, \fB--library-length\fP \fIINTEGER\fP
Expected library length. Default: autodetected. In range [1..inf].
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\fB-ld\fP, \fB--library-deviation\fP \fIINTEGER\fP
Deviation from the expected library length.                                             Default: autodetected. In range [1..inf].
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\fB-i\fP, \fB--indel-rate\fP \fIINTEGER\fP
Rescue unaligned ends within this percentual number of indels. In range [0..50]. Default: \fI25\fP.
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\fB-ni\fP, \fB--no-indels\fP
Turn off the rescue of unaligned ends containing indels.
.SS Performance Options:
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\fB-t\fP, \fB--threads\fP \fIINTEGER\fP
Specify the number of threads to use. In range [1..2048]. Default: \fI4\fP.