Sak

"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

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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]

Popular Predecessors

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Popular Successors

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.)

Workflows

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Links

Developers

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Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team
Plugin version: 2.4.1.202004061533
On NodePit since: 2022-12-06
Last update: 2024-12-23
KNIME versions: From v3.6 to v4.7

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