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

gustaf 1.4.1+dfsg                                 October 2014                                         GUSTAF(1)