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FastQC

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

Modern high throughput sequencers can generate tens of millions of sequences in a single run. Before analysing this sequence to draw biological conclusions you should always perform some simple quality control checks to ensure that the raw data looks good and there are no problems or biases in your data which may affect how you can usefully use it. This modified FastQC version (by Jonathan Hoser) automatically creates a filter file for filtering NGS read data. This filter file can be used by the RawReadManipulator to create filtered read files. In addition, the standard FastQC report is produced which provides a comprehensive overview about the read quality.
Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Options

Preference page

HTE
Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.

Input Ports

Icon
Cell 0: Path to ReadFile1
Cell 1 (Optional): Path to ReadFile2.

Output Ports

Icon
Cell 0: Path to ReadFile1
Cell 1 (Optional): Path to ReadFile2.
Cell 2: Path to FilterFile

Views

STDOUT / STDERR
The node offers a direct view of its standard out and the standard error of the tool.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

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Developers

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