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.