Abstract
Metagenomics, shotgun metagenomics in particular, is a field that has disproportionately benefited from advances in high-throughput sequencing technologies. This chapter discusses the choice of sample number, depth, and sequencing technology, the shearing, size-selection, and multiplexing options on Illumina platforms, and outlines the steps in the bioinformatic analysis and sharing of metagenomic data.
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References
Auer PL, Doerge RW (2010) Statistical design and analysis of RNA sequencing data. Genetics 185(2):405–416
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6(8):1621–1624
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38(6):1767–1771
Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota. Science 335(6068):587–590
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9(1):386–388
Rubin BE, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA (2013) Investigating the impact of storage conditions on microbial community composition in soil samples. PLoS One 8(7):e70460
Thomas T, Gilbert J, Meyer F (2012) Metagenomics—a guide from sampling to data analysis. Microb Inform Exp 2(1):3
Wang Y, Ghaffari N, Johnson CD, Braga-Neto UM, Wang H, Chen R, Zhou H (2011) Evaluation of the coverage and depth of transcriptome by RNA-seq in chickens. BMC Bioinformatics 12(Suppl 10):S5
Wilke A, Bischof J, Harrison T, Brettin T, D’Souza M, Gerlach W, Matthews H, Paczian T, Wilkening J, Glass EM, Desai N, Meyer F (2015) A RESTful API for accessing microbial community data for MG-RAST. PLoS Comput Biol 11(1):e1004008
Williams AG, Thomas S, Wyman SK, Holloway AK (2001) RNA-seq data: challenges in and recommendations for experimental design and analysis. Curr Protoc Hum Genet Unit 11.13(Suppl 83):11.13.1–11.13.20
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Trimble, W.L., Greenwald, S.M., Owens, S., Glass, E.M., Meyer, F. (2016). Metagenomic Design and Sequencing. In: Aransay, A., Lavín Trueba, J. (eds) Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer, Cham. https://doi.org/10.1007/978-3-319-31350-4_12
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DOI: https://doi.org/10.1007/978-3-319-31350-4_12
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