MUGAN: multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment

Abstract

Motivation: Metagenomic sequencing has become a crucial tool for obtaining a gene catalogue of operational taxonomic units (OTUs) in a microbial community. A typical metagenomic sequencing produces a large amount of data (often in the order of terabytes or more), and computational tools are indispensable for efficient processing. In particular, error correction in metagenomics is crucial for accurate and robust genetic cataloging of microbial communities. However, many existing error-correction tools take a prohibitively long time and often bottleneck the whole analysis pipeline. Results: To overcome this computational hurdle, we analyzed and exploited the data-level parallelism that exists in the error-correction procedure and proposed a tool named MUGAN that exploits both multi-core central processing units and multiple graphics processing units for co-processing. According to the experimental results, our approach reduced not only the time demand for denoising amplicons from approximately 59 h to only 46 min, but also the overestimation of the number of OTUs, estimating 6.7 times less species-level OTUs than the baseline. In addition, our approach provides web-based intuitive visualization of results. Given its efficiency and convenience, we anticipate that our approach would greatly facilitate denoising efforts in metagenomics studies.