title: CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.
abstract: BACKGROUND
  The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.
  
  
  RESULTS
  We introduce CLARK a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of CLARK is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode CLARK classifies, with high accuracy, about 32 million metagenomic short reads per minute. CLARK can also classify BAC clones or transcripts to chromosome arms and centromeric regions.
  
  
  CONCLUSIONS
  CLARK is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications. It is freely available at http://clark.cs.ucr.edu/ .
authors: Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside, USA. rouni001@cs.ucr.edu.
authors: Rachid
authors: R
authors: Ounit
authors: Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside, USA. steve.wanamaker@ucr.edu.
authors: Steve
authors: S
authors: Wanamaker
authors: Department of Plant & Botanic Sciences, University of California, 900 University Avenue, CA, 92521, Riverside, USA. timothy.close@ucr.edu.
authors: Timothy J
authors: TJ
authors: Close
authors: Department of Computer Science & Engineering, University of California, 900 University Avenue, CA, 92521, Riverside, USA. stelo@cs.ucr.edu.
authors: Stefano
authors: S
authors: Lonardi
mesh_terms: D000465:Algorithms; D023281:Genomics; D020407:Internet; D056186:Metagenomics; D014584:User-Computer Interface