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Stellar

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

STELLAR implements the SWIFT filter algorithm (Rasmussen et al., 2006) and a verification step for the SWIFT hits that applies local alignment, gapped X-drop extension, and extraction of the longest epsilon-match.

Input to STELLAR are two files, each containing one or more sequences in FASTA format. Each sequence from file 1 will be compared to each sequence in file 2. The sequences from file 1 are used as database, the sequences from file 2 as queries.

(c) 2010-2012 by Birte Kehr

Web Documentation for Stellar

Options

version-check
Turn this option off to disable version update notifications of the application.
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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[fa,fasta]
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[fa,fasta]

Output Ports

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Name of output file. [gff,txt]
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Name of output file for disabled query sequences. [fq,fastq,fa,fasta,faa,ffn,fna,frn,raw,sam]

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.2
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