journal article Open Access Apr 27, 2011

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

View at Publisher Save 10.1093/bib/bbr009
Topics

No keywords indexed for this article. Browse by subject →

References
28
[1]
Eisen PLoS biology (2007) 10.1371/journal.pbio.0050082
[2]
Rothberg Nature biotechnology (2008) 10.1038/nbt1485
[3]
The NIH Human Microbiome Project

Jane Peterson, Susan Garges, Maria Giovanni et al.

Genome Research 2009 10.1101/gr.096651.109
[4]
Altschul Journal of molecular biology (1990) 10.1006/jmbi.1990.9999
[5]
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

J. R. Cole, Q. Wang, E. Cardenas et al.

Nucleic Acids Research 2009 10.1093/nar/gkn879
[6]
Nucleic Acids Research (2009) 10.1093/nar/gkp285
[7]
Clustering of highly homologous sequences to reduce the size of large protein databases

Weizhong Li, Lukasz Jaroszewski, Adam Godzik

Bioinformatics 2001 10.1093/bioinformatics/17.3.282
[8]
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin et al.

Applied and Environmental Microbiology 2009 10.1128/aem.01541-09
[9]
Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

Bioinformatics 2010 10.1093/bioinformatics/btq461
[10]
Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

Patrick D. Schloss, Jo Handelsman

Applied and Environmental Microbiology 2005 10.1128/aem.71.3.1501-1506.2005
[11]
Environmental Microbiology (Print) (2009) 10.1111/j.1462-2920.2010.02193.x
[12]
BMC BIOINFOMATICS (2010) 10.1186/1471-2105-11-152
[13]
Nucleic Acids Research (2010) 10.1093/nar/gkq872
[14]
QIIME allows analysis of high-throughput community sequencing data

J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh et al.

Nature Methods 2010 10.1038/nmeth.f.303
[15]
Giongo (2010) 10.1038/ismej.2010.16
[17]
Microbial diversity in the deep sea and the underexplored “rare biosphere”

Mitchell L. Sogin, Hilary G. Morrison, Julie A. Huber et al.

Proceedings of the National Academy of Sciences 2006 10.1073/pnas.0605127103
[18]
Keijser Journal of Dental Research (2008) 10.1177/154405910808701104
[19]
MUSCLE: multiple sequence alignment with high accuracy and high throughput

R. C. Edgar

Nucleic Acids Research 2004 10.1093/nar/gkh340
[20]
MAFFT version 5: improvement in accuracy of multiple sequence alignment

K. Katoh

Nucleic Acids Research 2005 10.1093/nar/gki198
[21]
DeSantis Nucleic Acids Research (2006) 10.1093/nar/gkl244
[23]
Hierarchical Grouping to Optimize an Objective Function

Joe H. Ward

Journal of the American Statistical Association 1963 10.2307/2282967
[24]
A core gut microbiome in obese and lean twins

Peter J. Turnbaugh, Micah Hamady, Tanya Yatsunenko et al.

Nature 2009 10.1038/nature07540
[25]
[26]
[27]
Quince (2009) 10.1038/nmeth.1361
[28]
The Human Microbiome Project

Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady et al.

Nature 2007 10.1038/nature06244
Cited By
127
Metrics
127
Citations
28
References
Details
Published
Apr 27, 2011
Vol/Issue
13(1)
Pages
107-121
Cite This Article
Y. Sun, Y. Cai, S. M. Huse, et al. (2011). A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Briefings in Bioinformatics, 13(1), 107-121. https://doi.org/10.1093/bib/bbr009