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DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain a high degree of DNA sequences derived from hosts (plants, human) or other organisms of non-interest (arthropods, unicellular eukaryotes). This chapter presents a simple in silico method to r

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