Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nature Methods - Tập 10 Số 1 - Trang 57-59 - 2013
Nicholas A. Bokulich1, Sathish Subramanian2, Jeremiah J. Faith2, Dirk Gevers3, Jeffrey I. Gordon2, Rob Knight4, David A. Mills5, J. Gregory Caporaso6
1Department of Viticulture and Enology, University of California, Davis, Davis, California, USA
2Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri, USA
3Microbial Systems & Communities, Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
4Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
5Foods for Health Institute, University of California, Davis, Davis, California, USA.,
6Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, USA

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Tài liệu tham khảo

Yatsunenko, T. et al. Nature 486, 222–227 (2012).

Gilbert, J.A. & Meyer, F. ASM Microbe 7, 64–69 (2012).

Reeder, J. & Knight, R. Nat. Methods 7, 668–669 (2010).

Quince, C. et al. Nat. Methods 6, 639–641 (2009).

Caporaso, J.G. et al. Proc. Natl. Acad. Sci. USA 108, 4516–4522 (2011).

Minoche, A.E. et al. Genome Biol. 12, R112 (2011).

Caporaso, J.G. et al. Nat. Methods 7, 335–336 (2010).

Caporaso, J.G. et al. ISME J. 6, 1621–1624 (2012).

Bokulich, N.A. et al. PLoS ONE 7, e36357 (2012).

Bokulich, N.A., Bamforth, C.W. & Mills, D.A. PLoS ONE 7, e35507 (2012).

Lozupone, C. & Knight, R. Appl. Environ. Microbiol. 71, 8228–8235 (2005).

Edgar, R.C. Bioinformatics 26, 2460–2461 (2010).

Wang, Q., Garrity, G.M., Tiedje, J.M. & Cole, J.R. Appl. Environ. Microbiol. 73, 5261–5267 (2007).

DeSantis, T.Z. et al. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

Caporaso, J.G. et al. Bioinformatics 26, 266–267 (2010).