splazers - Split-map read sequences

       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.

       splazers - Split-map read sequences

-h, --help
              Display the help message.

       --version
              Display version information.

   MainOptions::-o, --outputOUTPUT_FILE
              Change output filename. Default: <READSFILE>.result.

       -f, --forward
              only compute forward matches

       -r, --reverse
              only compute reverse complement matches

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

       -rr, --recognition-rateDOUBLE
              set the 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].

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

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

       -ou, --outputUnmappedOUTPUT_FILE
              output filename for unmapped reads

       -v, --verbose
              verbose mode

       -vv, --vverbose
              very verbose mode

   OutputFormatOptions::-a, --alignment
              dump the alignment for each match

       -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)

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

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

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

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

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

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

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

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

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

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

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

   FiltrationOptions::-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.

splazers 1.3.8 [tarball]                                                                             SPLAZERS(1)

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.

splazers [OPTIONS] <GENOMEFILE> <READSFILE>
       splazers [OPTIONS] <GENOMEFILE> <READSFILE1> <READSFILE2>