Introduction

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.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.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.

Publications

  1. Accelerating metagenomic read classification on CUDA-enabled GPUs.
    Cite this
    Kobus R, Hundt C, Müller A, Schmidt B, 2017-01-01 - BMC bioinformatics

Credits

  1. Robin Kobus
    Developer

    Institute of Computer Science, Johannes Gutenberg University Mainz, Germany

  2. Christian Hundt
    Developer

    Institute of Computer Science, Johannes Gutenberg University Mainz, Germany

  3. André Müller
    Developer

    Institute of Computer Science, Johannes Gutenberg University Mainz, Germany

  4. Bertil Schmidt
    Investigator

    Institute of Computer Science, Johannes Gutenberg University Mainz, Germany

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Summary
AccessionBT005681
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByBertil Schmidt