참고문헌
- Ahn JH, Kim BY, Song J, Weon HY (2012) Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities J Microbiol 50:1071-1074 doi:10.1007/s12275-012-2642-z
- Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample Proceedings of the National Academy of Sciences of the United States of America 108 Suppl 1:4516-4522 doi:10.1073/pnas.1000080107
- Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis Nucleic Acids Res 37:D141-145 doi:10.1093/nar/gkn879
- Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Nucleic Acids Res 36:e105 doi:10.1093/nar/gkn425
- Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection Bioinformatics 27:2194-2200 doi:10.1093/bioinformatics/btr381
- Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermuller J (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures PLoS Comput Biol 5:e1000502 doi:10.1371/journal.pcbi.1000502
- Kennedy K, Hall MW, Lynch MD, Moreno-Hagelsieb G, Neufeld JD (2014a) Evaluating bias of illumina-based bacterial 16S rRNA gene profiles Appl Environ Microbiol 80:5717-5722 doi:10.1128/AEM.01451−14
- Kennedy NA, Walker AW, Berry SH, Duncan SH, Farquarson FM, Louis P, Thomson JM, Satsangi J, Flint HJ, Parkhill J, Lees CW, Hold GL (2014b) The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing PLoS One 9:e88982 doi:10.1371/journal.pone.0088982
- Kircher M, Stenzel U, Kelso J (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies Genome Biol 10:R83 doi:10.1186/gb-2009-10-8-r83
- Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform Applied and environmental microbiology 79:5112-5120 doi:10.1128/AEM.01043-13
- Kwon S, Park S, Lee B, Yoon S (2013) In-depth analysis of interrelation between quality scores and real errors in Illumina reads Conf Proc IEEE Eng Med Biol Soc 2013:635-638 doi:10.1109/EMBC.2013.6609580
- Li F, Hullar MA, Lampe JW (2007) Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota J Microbiol Methods 68:303-311 doi:10.1016/j.mimet.2006.09.006
- Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ (2012) Performance comparison of benchtop high-throughput sequencing platforms Nature biotechnology 30:434-439 doi:10.1038/nbt.2198
- Peng X, Yu KQ, Deng GH, Jiang YX, Wang Y, Zhang GX, Zhou HW (2013) Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags J Microbiol Methods 95:455-462 doi:10.1016/j.mimet.2013.07.015
- Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Nucleic Acids Res 41:D590-596 doi:10.1093/nar/gks1219
- Rapp D, Waller J, Brightwell G, Muirhead RW (2010) Lyophilization prior to direct DNA extraction from bovine feces improves the quantification of Escherichia coli O157:H7 and Campylobacter jejuni Appl Environ Microbiol 76:1686-1688 doi:10.1128/AEM.01866-09
- Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilic-Stojanovic M, Kekkonen RA, Palva A, de Vos WM (2010) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis J Microbiol Methods 81:127-134 doi:10.1016/j.mimet.2010.02.007
- Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C (2015) Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform Nucleic Acids Res 43:e37 doi:10.1093/nar/gku1341
- Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl Environ Microbiol 75:7537-7541 doi:10.1128/AEM.01541-09
- Unno T (2015) Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis J Microbiol Biotechnol 25:765-770 https://doi.org/10.4014/jmb.1409.09057
- Zhan A, Xiong W, He S, Macisaac HJ (2014) Influence of artifact removal on rare species recovery in natural complex communities using highthroughput sequencing PLoS One 9:e96928 doi:10.1371/journal.pone.0096928
- Zhang J, Kobert K, Flouri T, Stamatakis A (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR Bioinformatics 30:614-620 doi:10.1093/bioinformatics/btt593