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

Research output: Contribution to journalArticlepeer-review

Standard

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads. / Ahmed, Mohamed; Leys, Natalie; Raes, Jeroen; Monsieurs, Pieter.

In: BMC Bioinformatics, Vol. 16, No. 88, 15.03.2015, p. 1-15.

Research output: Contribution to journalArticlepeer-review

Author

Bibtex - Download

@article{9e9f5b4389174612862894409c499377,
title = "NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads",
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.",
keywords = "Error correction, Denoising, 16S rRNA amplicon sequencing, 454 pyrosequencing, Metagenomics",
author = "Mohamed Ahmed and Natalie Leys and Jeroen Raes and Pieter Monsieurs",
note = "Score = 10",
year = "2015",
month = mar,
day = "15",
doi = "10.1186/s12859-015-0520-5",
language = "English",
volume = "16",
pages = "1--15",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "Springer",
number = "88",

}

RIS - Download

TY - JOUR

T1 - NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads

AU - Ahmed, Mohamed

AU - Leys, Natalie

AU - Raes, Jeroen

AU - Monsieurs, Pieter

N1 - Score = 10

PY - 2015/3/15

Y1 - 2015/3/15

N2 - 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.

AB - 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.

KW - Error correction

KW - Denoising

KW - 16S rRNA amplicon sequencing

KW - 454 pyrosequencing

KW - Metagenomics

UR - http://ecm.sckcen.be/OTCS/llisapi.dll/open/ezp_138945

UR - http://knowledgecentre.sckcen.be/so2/bibref/12454

U2 - 10.1186/s12859-015-0520-5

DO - 10.1186/s12859-015-0520-5

M3 - Article

VL - 16

SP - 1

EP - 15

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - 88

ER -

ID: 363027