title: RTK: efficient rarefaction analysis of large datasets.
abstract: BACKGROUND
  The rapidly expanding microbiomics field is generating increasingly larger datasets, characterizing the microbiota in diverse environments. Although classical numerical ecology methods provide a robust statistical framework for their analysis, software currently available is inadequate for large datasets and some computationally intensive tasks, like rarefaction and associated analysis.
  
  
  RESULTS
  Here we present a software package for rarefaction analysis of large count matrices, as well as estimation and visualization of diversity, richness and evenness. Our software is designed for ease of use, operating at least 7x faster than existing solutions, despite requiring 10x less memory.
  
  
  METHODS
  C ++ and R source code (GPL v.2) as well as binaries are available from https://github.com/hildebra/Rarefaction and from CRAN (https://cran.r-project.org/).
  
  
  BACKGROUND
  bork@embl.de or falk.hildebrand@embl.de.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Structural & Computational Biology Unit, EMBL, 69117 Heidelberg, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Saary
authors.affiliation: Structural & Computational Biology Unit, EMBL, 69117 Heidelberg, Germany.
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Forslund
authors.affiliation: Structural & Computational Biology Unit, EMBL, 69117 Heidelberg, Germany.|MMPU, University of Heidelberg and European Molecular Biology Laboratory, 69117 Heidelberg, Germany.|Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany.|Department of Bioinformatics, University of Würzburg, 97074 Würzburg, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: Structural & Computational Biology Unit, EMBL, 69117 Heidelberg, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Hildebrand
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004777:Environment; D064307:Microbiota; D012984:Software