title: Accelerating metagenomic read classification on CUDA-enabled GPUs.
abstract: BACKGROUND
  Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed.
  
  
  RESULTS
  We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (CLARK) method. Using the processing power of a single Titan X GPU, cuCLARK can reach classification speeds of up to 50 million reads per minute. Corresponding speedups for species- (genus-)level classification range between 3.2 and 6.6 (3.7 and 6.4) compared to multi-threaded CLARK executed on a 16-core Xeon CPU workstation.
  
  
  CONCLUSIONS
  cuCLARK can perform metagenomic read classification at superior speeds on CUDA-enabled GPUs. It is free software licensed under GPL and can be downloaded at https://github.com/funatiq/cuclark free of charge.
authors.affiliation: Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany. rkobus@students.uni-mainz.de.
authors.forename: Robin
authors.initials: R
authors.lastname: Kobus
authors.affiliation: Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Hundt
authors.affiliation: Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.
authors.forename: André
authors.initials: A
authors.lastname: Müller
authors.affiliation: Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
mesh_terms: D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D056186:Metagenomics; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface
keywords: CUDA; Exact k-mer matching; GPUs; Metagenomics; Taxonomic assignment