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




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.


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:

-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.


gustaf version: 1.0 Last update July 2012

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