NAME

       splazers - Split-map read sequences

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.

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

       -rr, --recognition-rate DOUBLE
              set the 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].

       -mcl, --min-clipped-len INTEGER
              min. read length for read clipping In range [1..inf]. Default: 0.

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

       -ou, --outputUnmapped OUTPUT_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 INTEGER
              only consider matches with at most NUM more errors compared to  the  best  (default
              output all)

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

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

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

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

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

       -maxG, --max-gap INTEGER
              max. length of middle gap Default: 10000.

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

       -ep, --errors-prefix INTEGER
              max. number of errors in prefix match Default: 1.

       -es, --errors-suffix INTEGER
              max. number of errors in suffix match Default: 1.

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

   Filtration Options::
       -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.