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Stellar

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.

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

: [fa,fasta]
: [fa,fasta]

Output Ports

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

Popular Predecessors

Popular Successors

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.)

Workflows

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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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