Metagenomic sequencing has become a crucial tool for obtaining a gene catalogue of operational taxonomic units (OTUs) in a microbial community. High-throughput pyrosequencing is a next-generation sequencing technique very popular in microbial community analysis due to its longer read length compared to alternative methods. Computational tools are inevitable to process raw data from pyrosequencers, and in particular, noise removal is a critical data-mining step to obtain robust sequence reads. However, the slow rate of existing denoisers has bottlenecked the whole pyrosequencing process, let alone hindering efforts to improve robustness. To address these, we propose a new approach that can accelerate the denoising process substantially. By using our approach, it now takes only about 2 hours to denoise 62,873 pyrosequenced amplicons from a mixture of 91 full-length 16S rRNA clones. It would otherwise take nearly 2.5 days if existing software tools were used. Furthermore, our approach can effectively reduce overestimating the number of OTUs, producing 6.7 times fewer species-level OTUs on average than a state-of-theart alternative under the same condition. Leveraged by our approach, we hope that metagenomic sequencing will become an even more appealing tool for microbial community analysis.