.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH GUSTAF "1" "September 2014" "gustaf 1.4.1+dfsg" "User Commands"
.SH NAME
gustaf \- Gustaf \- Generic mUlti\-SpliT Alignment Finder: Tool for split\-read mapping allowing multiple splits.
.PP
SYNOPSIS
.IP
gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE>
.PP
DESCRIPTION
.IP
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.
.IP
The genome file is used as database input, the read file as query input.
.IP
All STELLAR options are supported. See STELLAR documentation for STELLAR
parameters and options.
.IP
(c) 2011\-2012 by Kathrin Trappe
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.IP
GUSTAF Options:
.IP
Main Options:
.HP
\fB\-tp\fR, \fB\-\-transPen\fR INT
.IP
Interchromosomal translocation penalty Default: 5.
.HP
\fB\-ip\fR, \fB\-\-invPen\fR INT
.IP
Inversion penalty Default: 5.
.HP
\fB\-op\fR, \fB\-\-orderPen\fR INT
.IP
Intrachromosomal order change penalty Default: 0.
.HP
\fB\-oth\fR, \fB\-\-overlapThresh\fR DOUBLE
.IP
Allowed overlap between matches Default: 0.5.
.HP
\fB\-gth\fR, \fB\-\-gapThresh\fR INT
.IP
Allowed gap length between matches Default: 10.
.HP
\fB\-ith\fR, \fB\-\-initGapThresh\fR INT
.IP
Allowed initial or ending gap length at begin and end of read
Default: 15.
.HP
\fB\-st\fR, \fB\-\-support\fR INT
.IP
Number of supporting reads Default: 2.
.IP
Input Options:
.HP
\fB\-m\fR, \fB\-\-matchfile\fR FILE
.IP
File of (stellar) matches Valid filetypes are: gff and GFF.
.IP
Output Options:
.HP
\fB\-bpo\fR, \fB\-\-breakpointOut\fR FILE
.IP
Name of breakpoint output file. Valid filetypes are: gff and txt.
Default: breakpoints.gff.
.HP
\fB\-j\fR, \fB\-\-jobName\fR STR
.IP
Job/Queue name Default: .
.HP
\fB\-do\fR, \fB\-\-dots\fR
.IP
Enable graph output in dot format
.IP
Stellar Options:
.IP
Main Options:
.HP
\fB\-e\fR, \fB\-\-epsilon\fR NUM
.IP
Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default:
0.05.
.HP
\fB\-l\fR, \fB\-\-minLength\fR NUM
.IP
Minimal length of epsilon\-matches. In range [0..inf]. Default: 100.
.HP
\fB\-f\fR, \fB\-\-forward\fR
.IP
Search only in forward strand of database.
.HP
\fB\-r\fR, \fB\-\-reverse\fR
.IP
Search only in reverse complement of database.
.HP
\fB\-a\fR, \fB\-\-alphabet\fR STR
.IP
Alphabet type of input sequences (dna, rna, dna5, rna5, protein,
char). One of dna, dna5, rna, rna5, protein, and char.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Set verbosity mode.
.IP
Filtering Options:
.HP
\fB\-k\fR, \fB\-\-kmer\fR NUM
.IP
Length of the q\-grams (max 32). In range [1..32].
.HP
\fB\-rp\fR, \fB\-\-repeatPeriod\fR NUM
.IP
Maximal period of low complexity repeats to be filtered. Default: 1.
.HP
\fB\-rl\fR, \fB\-\-repeatLength\fR NUM
.IP
Minimal length of low complexity repeats to be filtered. Default:
1000.
.HP
\fB\-c\fR, \fB\-\-abundanceCut\fR NUM
.IP
k\-mer overabundance cut ratio. In range [0..1]. Default: 1.
.IP
Verification Options:
.HP
\fB\-x\fR, \fB\-\-xDrop\fR NUM
.IP
Maximal x\-drop for extension. Default: 5.
.HP
\fB\-vs\fR, \fB\-\-verification\fR STR
.IP
Verification strategy: exact or bestLocal or bandedGlobal One of
exact, bestLocal, and bandedGlobal. Default: exact.
.HP
\fB\-dt\fR, \fB\-\-disableThresh\fR NUM
.IP
Maximal number of verified matches before disabling verification for
one query sequence (default infinity). In range [0..inf].
.HP
\fB\-n\fR, \fB\-\-numMatches\fR NUM
.IP
Maximal number of kept matches per query and database. If STELLAR
finds more matches, only the longest ones are kept. Default: 50.
.HP
\fB\-s\fR, \fB\-\-sortThresh\fR NUM
.IP
Number of matches triggering removal of duplicates. Choose a smaller
value for saving space. Default: 500.
.PP
VERSION
.IP
gustaf version: 1.0
Last update July 2012