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Sak

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

"It slices, it dices and it makes the laundry!"

Original SAK tool by David Weese. Rewrite by Manuel Holtgrewe.

Web Documentation for Sak

Options

version-check
Turn this option off to disable version update notifications of the application.
revcomp
Reverse-complement output.
max-length
Maximal number of sequence characters to write out.
sequence
Select the given sequence for extraction by 0-based index.
sequence-name
Select sequence with name prefix being NAME.
sequences
Select sequences from-to where from and to are 0-based indices.
infix
Select characters from-to where from and to are 0-based indices.
line-length
Set line length in output file. See section Line Length for details.

Input Ports

Icon
[fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Output Ports

Icon
Path to the resulting file. If omitted, result is printed to stdout in FastQ format. [fq,fastq,fa,fasta,faa,ffn,fna,frn,raw,sam]

Views

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

Best Friends (Outgoing)

Installation

To use this node in KNIME, install SeqAn from the following update site:

KNIME 4.3

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

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Developers

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