Robust computational analysis of rRNA hypervariable tag datasets

Maksim Sipos, Patricio Jeraldo, Nicholas D Chia, Ani Qu, A. Singh Dhillon, Michael E. Konkel, Karen E. Nelson, Bryan A. White, Nigel Goldenfeld

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Next-generation DNA sequencing is increasingly being utilized to probe microbial communities, such as gastrointestinal microbiomes, where it is important to be able to quantify measures of abundance and diversity. The fragmented nature of the 16S rRNA datasets obtained, coupled with their unprecedented size, has led to the recognition that the results of such analyses are potentially contaminated by a variety of artifacts, both experimental and computational. Here we quantify how multiple alignment and clustering errors contribute to overestimates of abundance and diversity, reflected by incorrect OUT assignment, corrupted phylogenies, inaccurate species diversity estimators, and rank abundance distribution functions. We show that straightforward procedural optimizations, combining preexisting tools, are effective in handling large (105{106) 16S rRNA datasets, and we describe metrics to measure the effectiveness and quality of the estimators obtained. We introduce two metrics to ascertain the quality of clustering of pyrosequenced rRNA data, and show that complete linkage clustering greatly outperforms other widely used methods.

Original languageEnglish (US)
Article numbere15220
JournalPLoS One
Volume5
Issue number12
DOIs
StatePublished - 2010
Externally publishedYes

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Biodiversity
Distribution functions
Cluster Analysis
ribosomal RNA
DNA
Phylogeny
DNA Sequence Analysis
Artifacts
linkage (genetics)
microbial communities
sequence analysis
species diversity
phylogeny
Datasets
methodology

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Sipos, M., Jeraldo, P., Chia, N. D., Qu, A., Dhillon, A. S., Konkel, M. E., ... Goldenfeld, N. (2010). Robust computational analysis of rRNA hypervariable tag datasets. PLoS One, 5(12), [e15220]. https://doi.org/10.1371/journal.pone.0015220

Robust computational analysis of rRNA hypervariable tag datasets. / Sipos, Maksim; Jeraldo, Patricio; Chia, Nicholas D; Qu, Ani; Dhillon, A. Singh; Konkel, Michael E.; Nelson, Karen E.; White, Bryan A.; Goldenfeld, Nigel.

In: PLoS One, Vol. 5, No. 12, e15220, 2010.

Research output: Contribution to journalArticle

Sipos, M, Jeraldo, P, Chia, ND, Qu, A, Dhillon, AS, Konkel, ME, Nelson, KE, White, BA & Goldenfeld, N 2010, 'Robust computational analysis of rRNA hypervariable tag datasets', PLoS One, vol. 5, no. 12, e15220. https://doi.org/10.1371/journal.pone.0015220
Sipos, Maksim ; Jeraldo, Patricio ; Chia, Nicholas D ; Qu, Ani ; Dhillon, A. Singh ; Konkel, Michael E. ; Nelson, Karen E. ; White, Bryan A. ; Goldenfeld, Nigel. / Robust computational analysis of rRNA hypervariable tag datasets. In: PLoS One. 2010 ; Vol. 5, No. 12.
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