title: Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.
abstract: BACKGROUND
  Many metagenomic studies compare hundreds to thousands of environmental and health-related samples by extracting and sequencing their 16S rRNA amplicons and measuring their similarity using beta-diversity metrics. However, one of the first steps--to classify the operational taxonomic units within the sample--can be a computationally time-consuming task because most methods rely on computing the taxonomic assignment of each individual read out of tens to hundreds of thousands of reads.
  
  
  RESULTS
  We introduce Quikr: a QUadratic, K-mer-based, Iterative, Reconstruction method, which computes a vector of taxonomic assignments and their proportions in the sample using an optimization technique motivated from the mathematical theory of compressive sensing. On both simulated and actual biological data, we demonstrate that Quikr typically has less error and is typically orders of magnitude faster than the most commonly used taxonomic assignment technique (the Ribosomal Database Project's Naïve Bayesian Classifier). Furthermore, the technique is shown to be unaffected by the presence of chimeras, thereby allowing for the circumvention of the time-intensive step of chimera filtering.
  
  
  BACKGROUND
  The Quikr computational package (in MATLAB, Octave, Python and C) for the Linux and Mac platforms is available at http://sourceforge.net/projects/quikr/.
authors.affiliation: Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43201, USA. koslicki.1@mbi.osu.edu
authors.forename: David
authors.initials: D
authors.lastname: Koslicki
authors.forename: Simon
authors.initials: S
authors.lastname: Foucart
authors.forename: Gail
authors.initials: G
authors.lastname: Rosen
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001499:Bayes Theorem; D002965:Classification / Q000379:methods; D056186:Metagenomics; D064307:Microbiota; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S