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SeqanFlexbar

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

SeqAn-Flexbar is a toolkit for the processing of sequenced NGS reads and based on the original Flexbar implementation of Dodt [1]. It is possible to demultiplex the reads and order them according to different kind of barcodes, to remove adapter contamination from reads, to trim low quality bases, filter N's or trim whole reads. The different tools are controlled through command line parameters and can operate on both single- and paired-end read data.

[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.

(c) Copyright 2008-2013 by Sebastian Roskosch.

Web Documentation for SeqanFlexbar

Options

records
Number of records to be read in one run.
noQualities
Force .fa format for output files.
threads
Number of threads used.
tag
Tags IDs of sequences which had adapters removed and/or were quality-trimmed.
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.
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.
no-adapter
Trim adapters from paired-end reads without using reference adapters.
no-paired
Trim paired-end input with single-end trimming method.
errors
Allowed errors in adapter detection.
overlap
Minimum length of overlap for a significant adapter match.
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.

Input Ports

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.]
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.]
FastA file containing the two adapter sequences. The adapters according to the layout: 5'-adapter1-read-adapter2-3'. [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.]
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

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]

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

Update Site

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