razers - Fast Read Mapping with Sensitivity Control

       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.

razersexample/genome.faexample/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.

       razersexample/genome.faexample/reads.faexample/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.

razers 1.5.8 [tarball]                                                                                 RAZERS(1)

       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.

       razers - Fast Read Mapping with Sensitivity Control

-h, --help
              Display the help message.

       --version
              Display version information.

   MainOptions:-f, --forward
              Map reads only to forward strands.

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

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

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

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

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

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

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

       -m, --max-hitsINTEGER
              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-readsINTEGER
              Trim reads to given length. Default: off. In range [14..inf].

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

       -v, --verbose
              Verbose mode.

       -vv, --vverbose
              Very verbose mode.

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

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

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

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

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

   FiltrationOptions:-s, --shapeSTRING
              Manually set k-mer shape. Default: 11111111111.

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

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

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

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

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

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

       -ed, --error-distrSTRING
              Write error distribution to FILE.

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

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

ARGUMENT0INPUT_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.

razers [OPTIONS] <GENOMEFILE> <READSFILE>
       razers [OPTIONS] <GENOMEFILE> <MP-READSFILE1> <MP-READSFILE2>