NAME

       gustaf  -  Gustaf  -  Generic  mUlti-SpliT  Alignment  Finder: Tool for split-read mapping
       allowing multiple splits.

       SYNOPSIS

              gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE>

       DESCRIPTION

              GUSTAF uses SeqAns STELLAR to find splits as local matches on different strands  or
              chromosomes. Criteria and penalties to chain these matches can be specified. Output
              file contains the breakpoints along the best chain.

              The genome file is used as database input, the read file as query input.

              All STELLAR options are supported. See STELLAR documentation for STELLAR parameters
              and options.

              (c) 2011-2012 by Kathrin Trappe

       -h, --help

              Displays this help message.

       --version

              Display version information

              GUSTAF Options:

              Main Options:

       -tp, --transPen INT

              Interchromosomal translocation penalty Default: 5.

       -ip, --invPen INT

              Inversion penalty Default: 5.

       -op, --orderPen INT

              Intrachromosomal order change penalty Default: 0.

       -oth, --overlapThresh DOUBLE

              Allowed overlap between matches Default: 0.5.

       -gth, --gapThresh INT

              Allowed gap length between matches Default: 10.

       -ith, --initGapThresh INT

              Allowed initial or ending gap length at begin and end of read Default: 15.

       -st, --support INT

              Number of supporting reads Default: 2.

              Input Options:

       -m, --matchfile FILE

              File of (stellar) matches Valid filetypes are: gff and GFF.

              Output Options:

       -bpo, --breakpointOut FILE

              Name  of  breakpoint  output  file.  Valid  filetypes  are:  gff and txt.  Default:
              breakpoints.gff.

       -j, --jobName STR

              Job/Queue name Default: .

       -do, --dots

              Enable graph output in dot format

              Stellar Options:

              Main Options:

       -e, --epsilon NUM

              Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.

       -l, --minLength NUM

              Minimal length of epsilon-matches. In range [0..inf]. Default: 100.

       -f, --forward

              Search only in forward strand of database.

       -r, --reverse

              Search only in reverse complement of database.

       -a, --alphabet STR

              Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One of dna,
              dna5, rna, rna5, protein, and char.

       -v, --verbose

              Set verbosity mode.

              Filtering Options:

       -k, --kmer NUM

              Length of the q-grams (max 32). In range [1..32].

       -rp, --repeatPeriod NUM

              Maximal period of low complexity repeats to be filtered. Default: 1.

       -rl, --repeatLength NUM

              Minimal length of low complexity repeats to be filtered. Default: 1000.

       -c, --abundanceCut NUM

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

              Verification Options:

       -x, --xDrop NUM

              Maximal x-drop for extension. Default: 5.

       -vs, --verification STR

              Verification  strategy: exact or bestLocal or bandedGlobal One of exact, bestLocal,
              and bandedGlobal. Default: exact.

       -dt, --disableThresh NUM

              Maximal number of verified matches before  disabling  verification  for  one  query
              sequence (default infinity). In range [0..inf].

       -n, --numMatches NUM

              Maximal  number  of  kept  matches  per  query  and database. If STELLAR finds more
              matches, only the longest ones are kept. Default: 50.

       -s, --sortThresh NUM

              Number of matches triggering removal of duplicates.  Choose  a  smaller  value  for
              saving space. Default: 500.

       VERSION

              gustaf version: 1.0 Last update July 2012