Fast, accurate error-correction of amplicon pyrosequences using Acacia

Lauren Bragg, Glenn Stone, Michael Imelfort, Philip Hugenholtz & Gene W Tyson

Microbial diversity metrics based on high-throughput amplicon sequencing are compromised by read errors. Roche 454 GS FLX Titanium pyrosequencing is currently the most widely used technology for amplicon-based microbial community studies, despite high homopolymer-associated insertion-deletion error rates1, 2. Currently, there are two software packages, AmpliconNoise3 and Denoiser4, that are commonly used to correct amplicon pyrosequencing errors. AmpliconNoise applies an approximate likelihood using empirically derived error distributions to remove pyrosequencing noise from reads. AmpliconNoise is highly effective at noise removal but is computationally intensive3. Denoiser is a faster algorithm that uses frequency-based heuristics rather than statistical modeling to cluster reads. Neither tool modifies individual reads; instead both select an 'error-free' read to represent reads in a given cluster.

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