Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.

Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs) is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referr...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Xiao-Tao Jiang, Hai Zhang, Hua-Fang Sheng, Yu Wang, Yan He, Fei Zou, Hong-Wei Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/310758fd66834024b6fa766db45ac085
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:310758fd66834024b6fa766db45ac085
record_format	dspace
spelling	oai:doaj.org-article:310758fd66834024b6fa766db45ac0852021-11-18T07:30:24ZTwo-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.1932-620310.1371/journal.pone.0030230https://doaj.org/article/310758fd66834024b6fa766db45ac0852012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22253923/?tool=EBIhttps://doaj.org/toc/1932-6203Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs) is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referred to as two-stage clustering (TSC) because it divides tags into two groups according to their abundance and clusters them sequentially. The more abundant group is clustered using a hierarchical algorithm similar to that in ESPRIT, which has a high degree of accuracy but is computationally costly for large datasets. The rarer group, which includes the majority of tags, is then heuristically clustered to improve efficiency. To further improve the computational efficiency and accuracy, two preclustering steps are implemented. To maintain clustering accuracy, all tags are grouped into an OTU depending on their pairwise Needleman-Wunsch distance. This method not only improved the computational efficiency but also mitigated the spurious OTU estimation from 'noise' sequences. In addition, OTUs clustered using TSC showed comparable or improved performance in beta-diversity comparisons compared to existing OTU selection methods. This study suggests that the distribution of sequencing datasets is a useful property for improving the computational efficiency and increasing the clustering accuracy of the high-throughput sequencing of PCR amplicons. The software and user guide are freely available at http://hwzhoulab.smu.edu.cn/paperdata/.Xiao-Tao JiangHai ZhangHua-Fang ShengYu WangYan HeFei ZouHong-Wei ZhouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e30230 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xiao-Tao Jiang Hai Zhang Hua-Fang Sheng Yu Wang Yan He Fei Zou Hong-Wei Zhou Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.
description	Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs) is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referred to as two-stage clustering (TSC) because it divides tags into two groups according to their abundance and clusters them sequentially. The more abundant group is clustered using a hierarchical algorithm similar to that in ESPRIT, which has a high degree of accuracy but is computationally costly for large datasets. The rarer group, which includes the majority of tags, is then heuristically clustered to improve efficiency. To further improve the computational efficiency and accuracy, two preclustering steps are implemented. To maintain clustering accuracy, all tags are grouped into an OTU depending on their pairwise Needleman-Wunsch distance. This method not only improved the computational efficiency but also mitigated the spurious OTU estimation from 'noise' sequences. In addition, OTUs clustered using TSC showed comparable or improved performance in beta-diversity comparisons compared to existing OTU selection methods. This study suggests that the distribution of sequencing datasets is a useful property for improving the computational efficiency and increasing the clustering accuracy of the high-throughput sequencing of PCR amplicons. The software and user guide are freely available at http://hwzhoulab.smu.edu.cn/paperdata/.
format	article
author	Xiao-Tao Jiang Hai Zhang Hua-Fang Sheng Yu Wang Yan He Fei Zou Hong-Wei Zhou
author_facet	Xiao-Tao Jiang Hai Zhang Hua-Fang Sheng Yu Wang Yan He Fei Zou Hong-Wei Zhou
author_sort	Xiao-Tao Jiang
title	Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.
title_short	Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.
title_full	Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.
title_fullStr	Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.
title_full_unstemmed	Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.
title_sort	two-stage clustering (tsc): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of pcr amplicons.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/310758fd66834024b6fa766db45ac085
work_keys_str_mv	AT xiaotaojiang twostageclusteringtscapipelineforselectingoperationaltaxonomicunitsforthehighthroughputsequencingofpcramplicons AT haizhang twostageclusteringtscapipelineforselectingoperationaltaxonomicunitsforthehighthroughputsequencingofpcramplicons AT huafangsheng twostageclusteringtscapipelineforselectingoperationaltaxonomicunitsforthehighthroughputsequencingofpcramplicons AT yuwang twostageclusteringtscapipelineforselectingoperationaltaxonomicunitsforthehighthroughputsequencingofpcramplicons AT yanhe twostageclusteringtscapipelineforselectingoperationaltaxonomicunitsforthehighthroughputsequencingofpcramplicons AT feizou twostageclusteringtscapipelineforselectingoperationaltaxonomicunitsforthehighthroughputsequencingofpcramplicons AT hongweizhou twostageclusteringtscapipelineforselectingoperationaltaxonomicunitsforthehighthroughputsequencingofpcramplicons
_version_	1718423338915725312

Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.

Ejemplares similares