NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads

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Abstract

The popularity of new sequencing technologies has led to an explosion of possible applications, including new approaches in biodiversity studies. However each of these sequencing technologies suffers from sequencing errors originating from different factors. For 16S rRNA metagenomics studies, the 454 pyrosequencing technology is one of the most frequently used platforms, but sequencing errors still lead to important data analysis issues (e.g. in clustering in taxonomic units and biodiversity estimation). The new error correction algorithm proposed in this work - NoDe (Noise Detector) - is trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read. The positive effect of NoDe in 16S rRNA studies was confirmed by the beneficial effect on the precision of the clustering of pyrosequencing reads in operational taxonomic units. NoDe was shown to be a computational efficient denoising algorithm for pyrosequencing reads, producing the lowest error rates in an extensive benchmarking study with other denoising algorithms.

Details

Original languageEnglish
Pages (from-to)1-15
JournalBMC Bioinformatics
Volume16
Issue number88
DOIs
Publication statusPublished - 15 Mar 2015

Keywords

  • Error correction, Denoising, 16S rRNA amplicon sequencing, 454 pyrosequencing, Metagenomics

ID: 363027