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

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
The main functions of FastQC are:

•Import of data from BAM, SAM or FastQ files (any variant)
•Providing a quick overview to tell you in which areas there may be problems
•Summary graphs and tables to quickly assess your data
•Export of results to an HTML based permanent report
•Offline operation to allow automated generation of reports without running the interactive application

Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/


Preference page

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

Input Ports

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

Output Ports

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


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

Best Friends (Incoming)

Best Friends (Outgoing)


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


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