Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

Microbiome

Volumn 1, Issue 1, 2013, Pages

  Fichot, Erin B ^a   Norman, R Sean ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

16S rRNA; Amplicon; Circular consensus sequence (ccs); Microbial diversity; PacBio; Pacific Biosciences

Indexed keywords

BIOINFORMATICS; CHIMERA; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC ENGINEERING AND GENE TECHNOLOGY; MICROBIAL GENOME; MICROBIAL PHYLOGENETIC PROFILING; NONHUMAN; NOTE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITY CONTROL; SCORING SYSTEM;

EID: 84878631963     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/2049-2618-1-10     Document Type: Note

References (18)

1. Loman NJ, Constantinidou C, Chan JZM, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 2012, 10(9):599-606. 10.1038/nrmicro2850, 22864262.
2. Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J 2012, 6(7):1273-1276. 10.1038/ismej.2011.186, 22170427.
3. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012, 30(7):692-700.
4. Marshall CW, Ross DE, Fichot EB, Norman RS, May HD. Electrosynthesis of commodity chemicals by an autotrophic microbial community. Appl Environ Microbiol 2012, 78(23):8412-8420. 10.1128/AEM.02401-12, 23001672.
5. Jumpstart Consortium Human Microbiome Project Data Generation Working Group Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One 2012, 7(6):e39315. 10.1371/journal.pone.0039315, 3374619, 22720093, Jumpstart Consortium Human Microbiome Project Data Generation Working Group.
6. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009, 75(23):7537-7541. 10.1128/AEM.01541-09, 2786419, 19801464.
7. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7(5):335-336. 10.1038/nmeth.f.303, 3156573, 20383131.
8. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 2011, 6(12):e27310. 10.1371/journal.pone.0027310, 3237409, 22194782.
9. Carneiro M, Russ C, Ross M, Gabriel S, Nusbaum C, DePristo M. Pacific Biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics 2012, 13(1):375. 10.1186/1471-2164-13-375, 3443046, 22863213.
10. von Wintzingerode F, Gobel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 1997, 21(3):213-229. 10.1111/j.1574-6976.1997.tb00351.x, 9451814.
11. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27(16):2194-2200. 10.1093/bioinformatics/btr381, 3150044, 21700674.
12. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012, 30:434-439. 10.1038/nbt.2198, 22522955.
13. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012, 2012:11.
14. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011, 11(5):759-769. 10.1111/j.1755-0998.2011.03024.x, 21592312.
15. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13:341. 10.1186/1471-2164-13-341, 3431227, 22827831.
16. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 10.1093/nar/gkn425, 2532726, 18660515.
17. Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 2012, 7(8):e43093. 10.1371/journal.pone.0043093, 3419673, 22905208.
18. Aird D, Ross MG, Chen W-S, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011, 12(2):R18. 10.1186/gb-2011-12-2-r18, 3188800, 21338519.