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SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements

Barbera, P.; Czech, L.; Lutteropp, S.; Stamatakis, Alexandros

Abstract:
Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny‐aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. ... mehr


Verlagsausgabe §
DOI: 10.5445/IR/1000125469
Veröffentlicht am 02.11.2020
Originalveröffentlichung
DOI: 10.1111/1755-0998.13255
Scopus
Zitationen: 2
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Theoretische Informatik (ITI)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2020
Sprache Englisch
Identifikator ISSN: 1471-8278, 1471-8286, 1755-098X, 1755-0998
KITopen-ID: 1000125469
Erschienen in Molecular ecology resources
Verlag John Wiley and Sons
Band 21
Heft 1
Seiten 340-349
Vorab online veröffentlicht am 29.09.2020
Schlagwörter diversity, microbiome, phylogenetic placement, species delimitation
Nachgewiesen in Web of Science
Scopus
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