Accurate determination of microbial diversity from 454 pyrosequencing data

Nature Methods

Volumn 6, Issue 9, 2009, Pages 639-641

  Quince, Christopher ^a   Lanzén, Anders ^b   Curtis, Thomas P ^c   Davenport, Russell J ^c   Hall, Neil ^d   Head, Ian M ^c   Read, L Fiona ^c   Sloan, William T ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b UNIVERSITY OF BERGEN   (Norway)

^c NEWCASTLE UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RNA 16S;

ACCURACY; AMPLICON; ARTICLE; DNA EXTRACTION; DNA SEQUENCE; GENE AMPLIFICATION; GENETIC ALGORITHM; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; RNA GENE;

ALGORITHMS; BACTERIA; GENETIC VARIATION; MODELS, GENETIC; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 69549112742     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1361     Document Type: Article

References (20)

1. Margulies, M. et al. Nature 437, 376-380 (2005).
2. Quinlan, A.R., Stewart, D.A., Stromberg, M.P. & Marth, G.T. Nat. Methods 5, 179-181 (2008).
3. Vacic, V., Jin, H., Zhu, J.-K. & Lonardi, S. Pac. Symp. Biocomput. 13, 75-86 (2008).
4. Fraley, C. & Raftery, A.E. Comput. J. 41, 578-588 (1998).
5. Schloss, P.D. & Handelsman, J. Appl. Environ. Microbiol. 71, 1501-1506 (2005).
6. Huber, J.A. et al. Science 318, 97-100 (2007).
7. Roesch, L.F. et al. ISME J. 1, 283-290 (2007).
8. Sogin, M.L. et al. Proc. Natl. Acad. Sci. USA 103, 12115-12120 (2006).
9. Quince, C., Curtis, T.P. & Sloan, W.T. ISME J. 2, 997-1006 (2008).
10. Wang, G.C.Y. & Wang, Y. Microbiology 142, 1107-1114 (1996).
11. Ashelford, K.E., Chuzhanova, N.A., Fry, J.C., Jones, A.J. & Weightman, A.J. Appl. Environ. Microbiol. 72, 5734-5741 (2006).
12. Cole, J.R. et al. Nucleic Acids Res. 37, D141-D145 (2009).
13. Liu, Z.Z., DeSantis, T.Z., Andersen, G.L. & Knight, R. Nucleic Acids Res. 36, 11 (2008).
14. Lozupone, C. & Knight, R. Appl. Environ. Microbiol. 71, 8228-8235 (2005).
15. Eriksson, N. et al. PLOS Comput. Biol. 4, 13 (2008).
16. Needleman, S.B. & Wunsch, C.D. J. Mol. Biol. 48, 443-453 (1970).
17. Katoh, K., Kuma, K., Toh, H. & Miyata, T. Nucleic Acids Res. 33 511-518 (2005).
18. Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L. & Mark Welch, D. Genome Biol. 8, 9 (2007).
19. Edgar, R.C. Nucleic Acids Res. 32, 1792-1797 (2004).
20. Altschul, S.F. et al. Nucleic Acids Res. 25, 3389-3402 (1997).