QIIME allows analysis of high-throughput community sequencing data

被引：28601

作者：

Caporaso, J. Gregory ^{[1
]}

Kuczynski, Justin ^{[2
]}

Stombaugh, Jesse ^{[1
]}

Bittinger, Kyle ^{[3
]}

Bushman, Frederic D. ^{[3
]}

Costello, Elizabeth K. ^{[1
]}

Fierer, Noah ^{[4
,5
]}

Pena, Antonio Gonzalez ^{[6
]}

Goodrich, Julia K. ^{[6
]}

Gordon, Jeffrey I. ^{[7
]}

Huttley, Gavin A. ^{[8
]}

Kelley, Scott T. ^{[9
]}

Knights, Dan ^{[6
]}

Koenig, Jeremy E. ^{[10
]}

Ley, Ruth E. ^{[10
]}

Lozupone, Catherine A. ^{[1
]}

McDonald, Daniel ^{[1
]}

Muegge, Brian D. ^{[7
]}

Pirrung, Meg ^{[1
]}

Reeder, Jens ^{[1
]}

Sevinsky, Joel R. ^{[11
]}

Tumbaugh, Peter J. ^{[7
]}

Walters, William A. ^{[2
]}

Widmann, Jeremy ^{[1
]}

Yatsunenko, Tanya ^{[7
]}

Zaneveld, Jesse ^{[2
]}

Knight, Rob ^{[1
,12
]}

机构：

[1] Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA

[2] Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USA

[3] Univ Penn, Dept Microbiol, Philadelphia, PA 19104 USA

[4] Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA

[5] Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO 80309 USA

[6] Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USA

[7] Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USA

[8] Australian Natl Univ, John Curtin Sch Med Res, Computat Genom Lab, Canberra, ACT 2601, Australia

[9] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA

[10] Cornell Univ, Dept Microbiol, Ithaca, NY USA

[11] Luca Technol, Golden, CO USA

[12] Univ Colorado, Howard Hughes Med Inst, Boulder, CO 80309 USA

来源：

NATURE METHODS | 2010年 / 7卷 / 05期

关键词：

PROJECT;

D O I：

10.1038/nmeth.f.303

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

引用

页码：335 / 336

页数：2

共 6 条

[1] The Ribosomal Database Project: improved alignments and new tools for rRNA analysis [J].

Cole, J. R. ;

Wang, Q. ;

Cardenas, E. ;

Fish, J. ;

Chai, B. ;

Farris, R. J. ;

Kulam-Syed-Mohideen, A. S. ;

McGarrell, D. M. ;

Marsh, T. ;

Garrity, G. M. ;

Tiedje, J. M. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D141-D145

[2] Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex [J].

Hamady, Micah ;

Walker, Jeffrey J. ;

Harris, J. Kirk ;

Gold, Nicholas J. ;

Knight, Rob .

NATURE METHODS, 2008, 5 (03) :235-237

[3] Ecology - Spying on nature [J].

Hopkin, Michael .

NATURE, 2006, 444 (7118) :420-421

[4] PyCogent: a toolkit for making sense from sequence [J].

Knight, Rob ;

Maxwell, Peter ;

Birmingham, Amanda ;

Carnes, Jason ;

Caporaso, J. Gregory ;

Easton, Brett C. ;

Eaton, Michael ;

Hamady, Micah ;

Lindsay, Helen ;

Liu, Zongzhi ;

Lozupone, Catherine ;

McDonald, Daniel ;

Robeson, Michael ;

Sammut, Raymond ;

Smit, Sandra ;

Wakefield, Matthew J. ;

Widmann, Jeremy ;

Wikman, Shandy ;

Wilson, Stephanie ;

Ying, Hua ;

Huttley, Gavin A. .

GENOME BIOLOGY, 2007, 8 (08)

[5] The NIH Human Microbiome Project [J].

Peterson, Jane ;

Garges, Susan ;

Giovanni, Maria ;

McInnes, Pamela ;

Wang, Lu ;

Schloss, Jeffery A. ;

Bonazzi, Vivien ;

McEwen, Jean E. ;

Wetterstrand, Kris A. ;

Deal, Carolyn ;

Baker, Carl C. ;

Di Francesco, Valentina ;

Howcroft, T. Kevin ;

Karp, Robert W. ;

Lunsford, R. Dwayne ;

Wellington, Christopher R. ;

Belachew, Tsegahiwot ;

Wright, Michael ;

Giblin, Christina ;

David, Hagit ;

Mills, Melody ;

Salomon, Rachelle ;

Mullins, Christopher ;

Akolkar, Beena ;

Begg, Lisa ;

Davis, Cindy ;

Grandison, Lindsey ;

Humble, Michael ;

Khalsa, Jag ;

Little, A. Roger ;

Peavy, Hannah ;

Pontzer, Carol ;

Portnoy, Matthew ;

Sayre, Michael H. ;

Starke-Reed, Pamela ;

Zakhari, Samir ;

Read, Jennifer ;

Watson, Bracie ;

Guyer, Mark .

GENOME RESEARCH, 2009, 19 (12) :2317-2323

[6] Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities [J].

Schloss, Patrick D. ;

Westcott, Sarah L. ;

Ryabin, Thomas ;

Hall, Justine R. ;

Hartmann, Martin ;

Hollister, Emily B. ;

Lesniewski, Ryan A. ;

Oakley, Brian B. ;

Parks, Donovan H. ;

Robinson, Courtney J. ;

Sahl, Jason W. ;

Stres, Blaz ;

Thallinger, Gerhard G. ;

Van Horn, David J. ;

Weber, Carolyn F. .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2009, 75 (23) :7537-7541

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