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.

              (c) Copyright 2009 by David Weese.

       -h, --help

              Displays this 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 NUM

              Percent identity threshold. In range [50..100]. Default: 92.

       -rr, --recognition-rate NUM

              Percent recognition rate. In range [80..100]. Default: 99.

       -pd, --param-dir DIR

              Read user-computed parameter files in the directory <DIR>.

       -id, --indels

              Allow indels. Default: mismatches only.

       -ll, --library-length NUM

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

       -le, --library-error NUM

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

       -m, --max-hits NUM

              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 NUM

              Trim reads to given length. Default: off. In range [14..inf].

       -o, --output FILE

              Change  output  filename.  Default:  <READS  FILE>.razers. Valid filetypes are: razers, eland, fa,
              fasta, and gff.

       -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 NUM

              Only consider matches with at most NUM more errors compared to the best. Default: output all.

       -gn, --genome-naming NUM

              Select how genomes are named (see Naming section below). In range [0..1]. Default: 0.

       -rn, --read-naming NUM

              Select how reads are named (see Naming section below). In range [0..2]. Default: 0.

       -so, --sort-order NUM

              Select how matches are sorted (see Sorting section below). In range [0..1]. Default: 0.

       -pf, --position-format NUM

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

              Filtration Options:

       -s, --shape BITSTRING

              Manually set k-mer shape. Default: 11111111111.

       -t, --threshold NUM

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

       -oc, --overabundance-cut NUM

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

       -rl, --repeat-length NUM

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

       -tl, --taboo-length NUM

              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 FILE

              Write error distribution to FILE.

       -mcl, --min-clipped-len NUM

              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.

       VERSION

              razers version: 1.2 [13764] Last update 2013-03-15