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SflexFilter

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

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

Icon
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

Icon
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.)

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