Nasko, Daniel JKoren, SergeyPhillippy, Adam MTreangen, Todd J2018-11-282018-11-282018-10-30Nasko, Daniel J, Koren, Sergey, Phillippy, Adam M, et al.. "RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification." (2018) BioMed Central: https://doi.org/10.1186/s13059-018-1554-6.https://hdl.handle.net/1911/103430Abstract In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes. These results suggest a need for new classification approaches specially adapted for large databases.This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Journal article2018-11-28https://doi.org/10.1186/s13059-018-1554-6enThe Author(s).