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GUSTAF(1) User Commands GUSTAF(1)

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
September 2014 gustaf 1.4.1+dfsg