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>

       gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE> <READ FASTA FILE 2>

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

REQUIRED ARGUMENTS

       FASTA_FILE_1 INPUT_FILE
               Valid filetypes are: .fq, .fastq, .fasta, and .fa.

       FASTA_FILE_2 List of INPUT_FILE's
              Either  one  (single-end) or two (paired-end) read files. Valid filetypes are: .fq,
              .fastq, .fasta, and .fa.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Main Options:
       -tp, --transPen INTEGER
              Interchromosomal translocation penalty Default: 5.

       -ip, --invPen INTEGER
              Inversion penalty Default: 5.

       -op, --orderPen INTEGER
              Intrachromosomal order change penalty Default: 0.

       -oth, --overlapThresh DOUBLE
              Allowed overlap between matches Default: 0.5.

       -gth, --gapThresh INTEGER
              Allowed gap length between matches, default value corresponse to expected  size  of
              microindels (5 bp) Default: 5.

       -ith, --initGapThresh INTEGER
              Allowed  initial  or  ending gap length at begin and end of read with no breakpoint
              (e.g. due to sequencing errors at the end) Default: 15.

       -bth, --breakendThresh INTEGER
              Allowed initial or ending gap length at begin  and  end  of  read  that  creates  a
              breakend/breakpoint (e.g. for reads extending into insertions) Default: 30.

       -tth, --tandemThresh INTEGER
              Minimal   length  of  (small)  insertion/duplication  with  double  overlap  to  be
              considered tandem repeat Default: 50.

       -pth, --breakpoint-pos-range INTEGER
              Allowed difference in breakpoint position Default: 5.

       -cbp, --complex-breakpoints
              Disable inferring complex SVs

       -st, --support INTEGER
              Number of supporting reads Default: 2.

       -mst, --mate-support INTEGER
              Number of supporting concordant mates Default: 2.

       -ll, --library-size INTEGER
              Library size of paired-end reads

       -le, --library-error INTEGER
              Library error (sd) of paired-end reads

       -rc, --revcompl
              Disable reverse complementing second mate pair input file.

   Input Options:
       -m, --matchfile INPUT_FILE
              File of (stellar) matches Valid filetypes are: .gff and .GFF.

   Output Options:
       -gff, --gffOut OUTPUT_FILE
              Name of gff breakpoint output file. Valid filetypes are: .txt  and  .gff.  Default:
              breakpoints.gff.

       -vcf, --vcfOut OUTPUT_FILE
              Name  of  vcf  breakpoint output file. Valid filetypes are: .vcf and .txt. Default:
              breakpoints.vcf.

       -j, --jobName STRING
              Job/Queue name Default: .

       -do, --dots
              Enable graph output in dot format

   Parallelization Options:
       -nth, --numThreads INTEGER
              Number of threads for parallelization of I/O. Default: 1.

   Main Options:
       -e, --epsilon DOUBLE
              Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.

       -l, --minLength INTEGER
              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 STRING
              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 INTEGER
              Length of the q-grams (max 32). In range [1..32].

       -rp, --repeatPeriod INTEGER
              Maximal period of low complexity repeats to be filtered. Default: 1.

       -rl, --repeatLength INTEGER
              Minimal length of low complexity repeats to be filtered. Default: 1000.

       -c, --abundanceCut DOUBLE
              k-mer overabundance cut ratio. In range [0..1]. Default: 1.

   Verification Options:
       -x, --xDrop DOUBLE
              Maximal x-drop for extension. Default: 5.

       -vs, --verification STRING
              Verification  strategy: exact or bestLocal or bandedGlobal One of exact, bestLocal,
              and bandedGlobal. Default: exact.

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

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

       -s, --sortThresh INTEGER
              Number of matches triggering removal of duplicates.  Choose  a  smaller  value  for
              saving space. Default: 500.