  In biomedical research, validation of a new scientific discovery is tied to
the reproducibility of its experimental results. However, in genomics, the
definition and implementation of reproducibility still remain imprecise. Here,
we argue that genomic reproducibility, defined as the ability of bioinformatics
tools to maintain consistent genomics results across technical replicates, is
key to generating scientific knowledge and enabling medical applications. We
first discuss different concepts of reproducibility and then focus on
reproducibility in the context of genomics, aiming to establish clear
definitions of relevant terms. We then focus on the role of bioinformatics
tools and their impact on genomic reproducibility and assess methods of
evaluating bioinformatics tools in terms of genomic reproducibility. Lastly, we
suggest best practices for enhancing genomic reproducibility, with an emphasis
on assessing the performance of bioinformatics tools through rigorous testing
across multiple technical replicates.
