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. 2012 Aug;6(8):1621-4.
doi: 10.1038/ismej.2012.8. Epub 2012 Mar 8.

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

J Gregory Caporaso  1 , Christian L Lauber, William A Walters, Donna Berg-Lyons, James Huntley, Noah Fierer, Sarah M Owens, Jason Betley, Louise Fraser, Markus Bauer, Niall Gormley, Jack A Gilbert, Geoff Smith, Rob Knight
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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

J Gregory Caporaso et al. ISME J. 2012 Aug.

Abstract

DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.

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Figures

Figure 1
Figure 1
Procrustes plots comparing: (a) 5′ reads from HiSeq lane 6 to 5′ reads from HiSeq lane 8; (b) 5′ reads from HiSeq lane 6 to 3′ reads from HiSeq lane 8; (c) 5′ reads from HiSeq lane 6 to 5′ MiSeq reads; (d) 5′ MiSeq reads to 3′ MiSeq reads. Lines connect paired samples.
See this image and copyright information in PMC

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References

    1. Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol. 2011;77:3846–3852. - PMC - PubMed
    1. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108 (Suppl 1:4516–4522. - PMC - PubMed
    1. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009;326:1694–1697. - PMC - PubMed
    1. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, et al. The Earth Microbiome Project: meeting report of the ‘1 EMP meeting on sample selection and acquisition' at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010;3:249–253. - PMC - PubMed
    1. Gower JC. Generalized procrustes analysis. Psychometrika. 1975;40:33–51.

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