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SflexFilter

This program is a sub-routine of SeqAn-Flexbar (a reimplementation of the original flexbar[1]) and can be used to filter reads and apply sequence independent trimming options

[1] Dodt, M.; Roehr, J.T.; Ahmed, R.; Dieterich, C. FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology 2012, 1, 895-905.

Web Documentation for SflexFilter

Options

records: Number of records to be read in one run.
noQualities: Force .fa format for output files.
threads: Number of threads used.
noInfo: Don't print paramter overwiev to console.
trimLeft: Number of Bases to be trimmed from the 5'end(s) before further processing.
trimRight: Number of Bases to be trimmed from the 3'end(s) before further processing.
minLength: Required minimal length of reads after all PREprocessing steps.
uncalled: Number of allowed uncalled bases per sequence.
substitute: Substitue Dna-character for N's.
finalMinLength: Deletes read (and mate) if on of them is shorter than the given value after the complete worflow.
finalLength: Trims reads to desired length after the complete workflow.

Input Ports

: Either one (single-end) or two (paired-end) read files. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2]

Output Ports

: Name of the output file. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,raw,raw.bgzf,raw.gz,raw.bz2,Inactive]

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SflexFilter Std Output: The text sent to standard out during the execution of SflexFilter.
SflexFilter Error Output: The text sent to standard error during the execution of SflexFilter. (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:

v3.7

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

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

Plugin version: 2.3.2.201707261654

On NodePit since: 2018-08-10

Last update: 2024-04-15

KNIME versions: From v3.6 to v3.7

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