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Gustaf

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.

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

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

Output Ports

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

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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.)

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Developers

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Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Plugin version: 2.4.1.202004061533

On NodePit since: 2022-12-06

Last update: 2024-04-13

KNIME versions: From v3.6 to v4.7

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