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 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selection of appropriate tools for specific applications. Finally, we present future challenges in the developing field of contamination detection.

Automated summary

The decreasing cost of sequencing and the increasing availability of publicly available genomes have created a need for automated software to assess genomic contamination. In the past six years, 18 programs have been published, each with its own strengths and weaknesses. This article reviews and benchmarks six of these programs, providing researchers with guidance in selecting appropriate tools for specific applications. It also highlights the future challenges in contamination detection.