Document of bibliographic reference 290102

BibliographicReference record

Type

Bibliographic resource

Type of document

Journal article

BibLvlCode

AS

Title

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare?

Abstract

BackgroundA key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies.ResultsWe provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT).ConclusionsWhile we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic.

WebOfScience code

https://www.webofscience.com/wos/woscc/full-record/WOS:000410194500006

Bibliographic citation

Balvociute, M.; Huson, D.H. (2017). SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? BMC Genom. 18(S2): 8. https://dx.doi.org/10.1186/s12864-017-3501-4

Is peer reviewed

true

Access rights

open access

Is accessible for free

true