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SflexDMulti

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 for demultiplexing of reads.

[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 SflexDMulti

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.
approximate
Select approximate barcode demultiplexing, allowing one mismatch.
hardClip
Select hardClip option, clipping the first length(barcode) bases in any case.
exclude
Exclude unidentified reads from further processing.

Input Ports

Icon
FastA file containing the used barcodes and their IDs. Necessary for demutiplexing. [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,opt.]
Icon
FastA/FastQ file containing the barcode for each read. [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,opt.]
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
Prefix and file ending of output files (prefix$.fa - $: placeholder which will be determined by the program.). [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]

Views

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

Developers

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