![]() While the exploration of single-nucleotide variation in a genome is a standard procedure in genomics, and many sophisticated tools exist to perform this task, identification of genetic variation in metagenomes remains challenging. ![]() With the aid of metagenomics, our understanding of the microbiome is moving from composition toward functionality, even down to the genetic variant level. ![]() Short-read metagenomic shotgun sequencing is currently the state-of-the-art technique for exploring these communities. Microbes live in complex communities that are of major importance for environmental ecology, public health, and animal physiology and pathology. 2Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.1Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.Augustijn 1, Alexandra Zhernakova 1 and Jingyuan Fu 1,2* Sergio Andreu-Sánchez 1,2, Lianmin Chen 1,2†, Daoming Wang 1†, Hannah E.
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