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.