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SflexQC

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 quality controlling 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 SflexQC

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.
quality
Quality threshold for read trimming.
length
Minimum read length after trimming. Shorter reads will be substituted by a single N or removed if the paired read is too short as well.
method
Method for trimming reads.
tag
Tags IDs of sequences which were quality-trimmed.

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]

Views

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