Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References
Daniel Hakim, Stephen Wandro, Karsten Zengler, Lívia S. Zaramela, Brent Nowinski, Austin D. Swafford, Qiyun Zhu, Se Jin Song, Antonio González, Daniel McDonald, Rob Knight
Abstract
Taxonomic assignment, assigning sequences to specific taxonomic units, is a crucial processing step in microbiome analyses. Issues in taxonomic assignment affect interpretation of what microbes are present in each sample and may be associated with specific environmental or clinical conditions. Assigning importance to a particular taxon relies strongly on independence of assigned counts. The false inclusion of thousands of correlated taxa makes interpretation ambiguous, leading to underconstrained results which cannot be reproduced. The importance sometimes attached to implausible artifacts such as anthrax or bubonic plague is especially problematic. We show that the Zebra filter retrieves only the nearest relatives of sample contents enabling more reproducible and biologically plausible interpretation of metagenomic data.