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Allows to obtain biological insight into genetic events investigated by exome sequencing. Simplex is an automatized pipeline for investigating exome single-end (SE) and paired-end (PE) sequencing data generated by deep sequencing devices from Illumina and ABI SOLiD. The pipeline combines published and in-house developed applications and is continuously, automatically tested. Simplex is provided as a ready to use VirtualBox image and a fully configured Cloud image.

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SIMPLEX classification

SIMPLEX specifications

Software type:
Restrictions to use:
Input format:
GNU Affero General Public License version 3
Command line interface
Input data:
The raw sequence reads, their corresponding base calling quality values, and a list of genomic positions specifying the complete exome.
Output data:
A detailed summary report, files that can be used for viewing mapping results in Genome Browsers, and annotated lists of variants, which can be easily opened with office programs.
Computer skills:

SIMPLEX distribution


SIMPLEX support



This tool is not maintained anymore.


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Division for Bioinformatics, Biocenter, Innsbruck Medical University, Innsbruck, Austria; Oncotyrol, Center for Personalized Cancer Medicine, Innsbruck, Austria; Division of Human Genetics, Biocenter, Innsbruck Medical University, Innsbruck, Austria

Funding source(s)

Supported by GENAU Bioinformatics Network (BIN III), by the "Bioinformatics Tyrol" project of the "Standortagentur Tyrol," and by the COMET Center ONCOTYROL.

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