NAME

       yara_mapper - Yara Mapper

SYNOPSIS

       yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <SE-READS FILE>
       yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <PE-READS FILE 1> <PE-READS FILE 2>

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_INDEX_PREFIX INPUT_PREFIX
              An indexed reference genome.

       READS_FILE List of INPUT_FILE's
              Either  one  single-end  or  two paired-end / mate-pair read files. 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 global statistics.

       -vv, --very-verbose
              Displays extensive statistics for each batch of reads.

   Output Options:
       -o, --output-file OUTPUT_FILE
              Specify an output file. Default: write the file to standard output. Valid filetypes
              are:  .sam[.*]  and  .bam, where * is any of the following extensions: gz, bz2, and
              bgzf for transparent (de)compression.

       -f, --output-format STRING
              Specify    an    output    format.    Note:    when    specifying    the     option
              --output-file,    the    output    format    is    taken    from    the    filename
              extension. One of bam, sam, sam.bgzf, sam.gz, and sam.bz2. Default: sam.

       -rg, --read-group STRING
              Specify a read group for all records in the SAM/BAM file. Default: none.

       -sa, --secondary-alignments STRING
              Specify      whether      to       output       secondary       alignments       in
              the      XA      tag      of     the     primary     alignment,     as     separate
              secondary records, or to omit them. One of tag, record, and omit. Default: tag.

       -ra, --rabema-alignments
              Output            alignments            compatible             with             the
              Read Alignment BEnchMArk (RABEMA).

   Mapping Options:
       -e, --error-rate INTEGER
              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: 5.

       -s, --strata-rate INTEGER
              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: 0.

       -y, --sensitivity STRING
              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 low, high, and full. Default: high.

   Paired-End Mapping Options:
       -ll, --library-length INTEGER
              Expected library length. Default: autodetected. In range [1..inf].

       -ld, --library-deviation INTEGER
              Deviation         from         the         expected         library         length.
              Default: autodetected. In range [1..inf].

       -i, --indel-rate INTEGER
              Rescue unaligned ends within this percentual number of indels.  In  range  [0..50].
              Default: 25.

       -ni, --no-indels
              Turn off the rescue of unaligned ends containing indels.

   Performance Options:
       -t, --threads INTEGER
              Specify the number of threads to use. In range [1..2048]. Default: 4.