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NAME

       razers - Fast Read Mapping with Sensitivity Control

SYNOPSIS

       razers [OPTIONS] <GENOME FILE> <READS FILE>
       razers [OPTIONS] <GENOME FILE> <MP-READS FILE1> <MP-READS FILE2>

DESCRIPTION

       RazerS  is  a  versatile  full-sensitive  read mapper based on a k-mer counting filter. It
       supports single and paired-end mapping, and optimally parametrizes the filter based  on  a
       user-defined   minimal   sensitivity.  See  http://www.seqan.de/projects/razers  for  more
       information.

       Input to RazerS is a reference genome file and either one file with  single-end  reads  or
       two  files  containing  left  or right mates of paired-end reads. Use - to read single-end
       reads from stdin.

       (c) Copyright 2009 by David Weese.

REQUIRED ARGUMENTS

       ARGUMENT 0 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.

       READS List of INPUT_FILE's
              Either  one  (single-end)  or  two  (paired-end)  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.

   Main Options:
       -f, --forward
              Map reads only to forward strands.

       -r, --reverse
              Map reads only to reverse strands.

       -i, --percent-identity DOUBLE
              Percent identity threshold. In range [50..100]. Default: 92.

       -rr, --recognition-rate DOUBLE
              Percent recognition rate. In range [80..100]. Default: 99.

       -pd, --param-dir STRING
              Read user-computed parameter files in the directory <DIR>.

       -id, --indels
              Allow indels. Default: mismatches only.

       -ll, --library-length INTEGER
              Paired-end library length. In range [1..inf]. Default: 220.

       -le, --library-error INTEGER
              Paired-end library length tolerance. In range [0..inf]. Default: 50.

       -m, --max-hits INTEGER
              Output only <NUM> of the best hits. In range [1..inf]. Default: 100.

       --unique
              Output only unique best matches (-m 1 -dr 0 -pa).

       -tr, --trim-reads INTEGER
              Trim reads to given length. Default: off. In range [14..inf].

       -o, --output OUTPUT_FILE
              Change output filename (use - to dump to stdout in razers format). Default:  <READS
              FILE>.razers. Valid filetypes are: .razers, .gff, .fasta, .fa, and .eland.

       -v, --verbose
              Verbose mode.

       -vv, --vverbose
              Very verbose mode.

   Output Format Options:
       -a, --alignment
              Dump the alignment for each match (only razer or fasta format).

       -pa, --purge-ambiguous
              Purge reads with more than <max-hits> best matches.

       -dr, --distance-range INTEGER
              Only  consider  matches with at most NUM more errors compared to the best. Default:
              output all.

       -gn, --genome-naming INTEGER
              Select how genomes are named (see Naming section below). In range [0..1].  Default:
              0.

       -rn, --read-naming INTEGER
              Select how reads are named (see Naming section below). In range [0..2]. Default: 0.

       -so, --sort-order INTEGER
              Select  how  matches  are  sorted  (see  Sorting  section  below). In range [0..1].
              Default: 0.

       -pf, --position-format INTEGER
              Select begin/end position  numbering  (see  Coordinate  section  below).  In  range
              [0..1]. Default: 0.

   Filtration Options:
       -s, --shape STRING
              Manually set k-mer shape. Default: 11111111111.

       -t, --threshold INTEGER
              Manually set minimum k-mer count threshold. In range [1..inf].

       -oc, --overabundance-cut INTEGER
              Set k-mer overabundance cut ratio. In range [0..1].

       -rl, --repeat-length INTEGER
              Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.

       -tl, --taboo-length INTEGER
              Set taboo length. In range [1..inf]. Default: 1.

       -lm, --low-memory
              Decrease memory usage at the expense of runtime.

   Verification Options:
       -mN, --match-N
              N matches all other characters. Default: N matches nothing.

       -ed, --error-distr STRING
              Write error distribution to FILE.

       -mcl, --min-clipped-len INTEGER
              Set minimal read length for read clipping. In range [0..inf]. Default: 0.

       -qih, --quality-in-header
              Quality string in fasta header.

FORMATS, NAMING, SORTING, AND COORDINATE SCHEMES

       RazerS  supports  various output formats. The output format is detected automatically from
       the file name suffix.

       .razers
              Razer format

       .fa, .fasta
              Enhanced Fasta format

       .eland Eland format

       .gff   GFF format

              By default, reads and contigs are referred by their Fasta ids given  in  the  input
              files. With the -gn and -rn options this behaviour can be changed:

       0      Use Fasta id.

       1      Enumerate beginning with 1.

       2      Use the read sequence (only for short reads!).

              The  way  matches  are sorted in the output file can be changed with the -so option
              for the following formats: razer, fasta, sam, and amos. Primary and secondary  sort
              keys are:

       0      1. read number, 2. genome position

       1      1. genome position, 2. read number

              The  coordinate  space used for begin and end positions can be changed with the -pf
              option for the razer and fasta formats:

       0      Gap space. Gaps between characters are counted from 0.

       1      Position space. Characters are counted from 1.

EXAMPLES

       razers example/genome.fa example/reads.fa -id -a -mN -v
              Map single-end reads with 4% error rate, indels, and output the alignments. Ns  are
              considered to match everything.

       razers example/genome.fa example/reads.fa example/reads2.fa -id -mN
              Map  paired-end  reads with up to 4% errors, indels, and output concordantly mapped
              pairs within default library size. Ns are considered to match everything.