CLEVER, short for Clique-Enumerating Variant Finder, implements an extremely fast methodology for discovering genetic variants in genome fragment data. What makes it unique is that this software allows for the discovery of genetic variants that traditionally were hard to detect due to algorithmic challenges. These so-called "twilight zone variants", also know as the "dark matter of human DNA", require ultra-fast algorithms able to process the large genome data – amounting to several hundreds of Gigabytes for one individual – in reasonable time.

The processing speed of the CLEVER software allows it to be used in population-scale sequencing projects, such as the 'Genome of the Netherlands' project where the genome data for a few thousand individuals can amount to petabytes of information. Other users are researchers from computer science institutions, medical centers, hospitals, and some pharmaceutical companies.

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More details on the algorithms underlying our tools can be found in the following papers. If you use our tools for your research, please cite us.

Tobias Marschall, Ivan Costa, Stefan Canzar, Markus Bauer, Gunnar Klau, Alexander Schliep and Alexander Schoenhuth. CLEVER: Clique-Enumerating Variant Finder. Bioinformatics, 28(22), pages 2875-2882, 2012. DOI: 10.1093/bioinformatics/bts566.

Tobias Marschall and Alexander Schönhuth. LASER: Sensitive Long-Indel-Aware Alignment of Sequencing Reads. arXiv: 1303.3520.

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Citation
Schönhuth, A. (2015). CLEVER.