NAME

       splazers ========

       SYNOPSIS

              splazers  [OPTIONS]  <GENOME  FILE>  <READS  FILE> splazers [OPTIONS] <GENOME FILE>
              <READS FILE 1> <READS FILE 2>

       DESCRIPTION

              SplazerS uses a prefix-suffix mapping strategy to split-map read sequences.If a SAM
              file  of  mapped  reads  is  given  as  input,  all  unmapped but anchoredreads are
              split-mapped onto anchoring target regions (specify option -an),if a  Fasta/q  file
              of reads is given, reads are split-mapped onto the wholereference sequence.

              (c) Copyright 2010 by Anne-Katrin Emde.

       -h, --help

              Displays this help message.

       --version

              Display version information

              Main Options::

       -o, --output FILE

              Change output filename. Default: <READS FILE>.result.

       -f, --forward

              only compute forward matches

       -r, --reverse

              only compute reverse complement matches

       -i, --percent-identity NUM

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

       -rr, --recognition-rate NUM

              set the 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].

       -mcl, --min-clipped-len NUM

              min. read length for read clipping In range [1..inf]. Default: 0.

       -qih, --quality-in-header

              quality string in fasta header

       -ou, --outputUnmapped FILE

              output filename for unmapped reads

       -v, --verbose

              verbose mode

       -vv, --vverbose

              very verbose mode

              Output Format Options::

       -a, --alignment

              dump the alignment for each match

       -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)

       -of, --output-format NUM

              Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM.  In
              range [0..4].

       -gn, --genome-naming NUM

              Select  how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In
              range [0..1]. Default: 0.

       -rn, --read-naming NUM

              Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning  with  1.  In
              range [0..1]. Default: 0.

       -so, --sort-order NUM

              Select  how  matches  are  sorted.  0 = read number, 1 = genome position.  In range
              [0..1]. Default: 0.

       -pf, --position-format NUM

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

              Split Mapping Options::

       -sm, --split-mapping NUM

              min.  match  length  for prefix/suffix mapping (to disable split mapping, set to 0)
              Default: 18.

       -maxG, --max-gap NUM

              max. length of middle gap Default: 10000.

       -minG, --min-gap NUM

              min. length of middle gap (for edit distance mapping about 10% of  read  length  is
              recommended) Default: 0.

       -ep, --errors-prefix NUM

              max. number of errors in prefix match Default: 1.

       -es, --errors-suffix NUM

              max. number of errors in suffix match Default: 1.

       -gl, --genome-len NUM

              genome  length in Mb, for computation of expected number of random matches In range
              [-inf..10000]. Default: 3000.

       -an, --anchored

              anchored split mapping, only unmapped reads with mapped mates will  be  considered,
              requires the reads to be given in SAM format

       -pc, --penalty-c NUM

              percent of read length, used as penalty for split-gap Default: 2.

              Filtration Options::

       -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.

       VERSION

              splazers version: 1.1 Last update Apr 2011