Contamination detection in genomic data: more is not enough

The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last six years, 18 programs have been pub-lished, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algo-rithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selec-tion of appropriate tools for specific applications. Finally, we present future chal-lenges in the developing field of contamination detection.