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Gustaf

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

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

Web Documentation for Gustaf

Options

version-check
Turn this option off to disable version update notifications of the application.
transPen
Interchromosomal translocation penalty
invPen
Inversion penalty
orderPen
Intrachromosomal order change penalty
overlapThresh
Allowed overlap between matches
gapThresh
Allowed gap length between matches, default value corresponse to expected size of microindels (5 bp)
initGapThresh
Allowed initial or ending gap length at begin and end of read with no breakpoint (e.g. due to sequencing errors at the end)
breakendThresh
Allowed initial or ending gap length at begin and end of read that creates a breakend/breakpoint (e.g. for reads extending into insertions)
tandemThresh
Minimal length of (small) insertion/duplication with double overlap to be considered tandem repeat
breakpoint-pos-range
Allowed difference in breakpoint position
complex-breakpoints
Disable inferring complex SVs
support
Number of supporting reads
mate-support
Number of supporting concordant mates
library-size
Library size of paired-end reads
library-error
Library error (sd) of paired-end reads
revcompl
Disable reverse complementing second mate pair input file.
jobName
Job/Queue name
dots
Enable graph output in dot format
numThreads
Number of threads for parallelization of I/O.
epsilon
Maximal error rate (max 0.25).
minLength
Minimal length of epsilon-matches.
forward
Search only in forward strand of database.
reverse
Search only in reverse complement of database.
alphabet
Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char).
verbose
Set verbosity mode.
kmer
Length of the q-grams (max 32).
repeatPeriod
Maximal period of low complexity repeats to be filtered.
repeatLength
Minimal length of low complexity repeats to be filtered.
abundanceCut
k-mer overabundance cut ratio.
xDrop
Maximal x-drop for extension.
verification
Verification strategy: exact or bestLocal or bandedGlobal
disableThresh
Maximal number of verified matches before disabling verification for one query sequence (default infinity).
numMatches
Maximal number of kept matches per query and database. If STELLAR finds more matches, only the longest ones are kept.
sortThresh
Number of matches triggering removal of duplicates. Choose a smaller value for saving space.

Input Ports

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File of (stellar) matches [gff,GFF,opt.]
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[fa,fasta,fq,fastq]
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Either one (single-end) or two (paired-end) read files. [fa,fasta,fq,fastq]

Output Ports

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Name of gff breakpoint output file. [gff,txt]
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Name of vcf breakpoint output file. [vcf,txt]

Views

Gustaf Std Output
The text sent to standard out during the execution of Gustaf.
Gustaf Error Output
The text sent to standard error during the execution of Gustaf. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Installation

To use this node in KNIME, install SeqAn from the following update site:

KNIME 4.2
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