  The assessment of microbial species biodiversity is essential in ecology and
evolutionary biology (Reaka-Kudla et al. 1996), but especially challenging for
communities of microorganisms found in the environment (Das et al. 2006,
Hillebrand et al. 2018). Beyond providing a census of organisms in the ocean,
assessing marine microbial biodiversity can reveal how microbes respond to
environmental change (Salazar et al. 2017), clarify the ecological roles of
community members (Hehemann et al. 2016), and lead to biotechnology discoveries
(Das et al. 2006). Computational approaches to characterize taxonomic diversity
and phylogeny based on the quality of available data for environmental sequence
datasets is fundamental for advancing our understanding of the role of these
organisms in the environment. Even more pressing is the need for comprehensive
and consistent methods to assign taxonomy to environmentally-relevant microbial
eukaryotes. Here, we present EUKulele, an open-source software tool designed to
assign taxonomy to microeukaryotes detected in meta-omic samples, and
complement analysis approaches in other domains by accommodating assembly
output and providing concrete metrics reporting the taxonomic completeness of
each sample.
