Genomic reproducibility in the bioinformatics era
Pelin Icer Baykal, Paweł P. Łabaj, Florian Markowetz, Lynn M. Schriml, Daniel J. Stekhoven, Serghei Mangul, Niko Beerenwinkel
Abstract
In biomedical research, validating a scientific discovery hinges on the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility remain imprecise. We argue that genomic reproducibility, defined as the ability of bioinformatics tools to maintain consistent results across technical replicates, is essential for advancing scientific knowledge and medical applications. Initially, we examine different interpretations of reproducibility in genomics to clarify terms. Subsequently, we discuss the impact of bioinformatics tools on genomic reproducibility and explore methods for evaluating these tools regarding their effectiveness in ensuring genomic reproducibility. Finally, we recommend best practices to improve genomic reproducibility.