CuCLARK is a metagenomic classifier for CUDA-enabled GPUs, based on CLARK http://clark.cs.ucr.edu/). The program comes in two variants: CuCLARK and CuCLARK-l. CuCLARK is designed for workstations which can provide enough RAM to fit large databases (like all bacterial genomes in NCBI/RefSeq) and an arbitrary number of CUDA-enabled GPUs. CuCLARK-l uses a much smaller database and can be run on computers with 4 GB of RAM and a CUDA-enabled GPU with at least 1 GB of memory.
- André Müller, Christian Hundt, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt (2017);
MetaCache: Context-aware classification of metagenomic reads using minhashing, Bioinformatics, btx520, https://doi.org/10.1093/bioinformatics/btx520
Kobus R, Hundt C, Müller A, and Schmidt, B (2017)
Accelerating metagenomic read classification on CUDA-enabled GPUs
BMC Bioinformatics, DOI 10.1186/s12859-016-1434-6