N. Desai, D. Antonopoulos, J. Gilbert, E. Glass, and F. Meyer, From genomics to metagenomics, Current Opinion in Biotechnology, vol.23, issue.1, pp.72-76, 2012.
DOI : 10.1016/j.copbio.2011.12.017

D. Johnson, A. Mortazavi, R. Myers, and B. Wold, Genome-Wide Mapping of in Vivo Protein-DNA Interactions, Science, vol.316, issue.5830, pp.3161497-502, 2007.
DOI : 10.1126/science.1141319

D. Licatalosi, A. Mele, J. Fak, J. Ule, M. Kayikci et al., HITS-CLIP yields genome-wide insights into brain alternative RNA processing, Nature, vol.8, issue.7221, pp.456464-469, 2008.
DOI : 10.1038/nature07488

J. Davey and M. Blaxter, RADSeq: next-generation population genetics, Briefings in Functional Genomics, vol.9, issue.5-6, pp.5-6416
DOI : 10.1093/bfgp/elq031
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080771

J. Wooley, A. Godzik, and I. Friedberg, A Primer on Metagenomics, PLoS Computational Biology, vol.14, issue.2, p.1000667, 2010.
DOI : 10.1371/journal.pcbi.1000667.t002
URL : http://doi.org/10.1371/journal.pcbi.1000667

R. Amann, W. Ludwig, and K. Schleifer, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev, vol.59, pp.143-169, 1995.

D. Mende, A. Waller, S. Sunagawa, A. Jäelin, M. Chan et al., Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data, PLoS ONE, vol.27, issue.2, p.31386
DOI : 10.1371/journal.pone.0031386.s003

Y. Wang, H. Leung, S. Yiu, and F. Chin, MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species, Journal of Computational Biology, vol.19, issue.2, pp.241-249
DOI : 10.1089/cmb.2011.0276

V. Markowitz, I. Chen, K. Chu, E. Szeto, K. Palaniappan et al., NC: IMG/M: the integrated metagenome data management and comparative analysis system, Nucleic Acids Res, 2011.

D. Huson, A. Auch, J. Qi, and S. Schuster, MEGAN analysis of metagenomic data, Genome Research, vol.17, issue.3, pp.377-386, 2007.
DOI : 10.1101/gr.5969107

K. Foerstner, V. Mering, C. Hooper, S. Bork, and P. , Environments shape the nucleotide composition of genomes, EMBO reports, vol.33, issue.12, pp.1208-1213, 2005.
DOI : 10.1126/science.1093857

J. Raes, J. Korbel, M. Lercher, C. Von-mering, and P. Bork, Prediction of effective genome size in metagenomic samples, Genome Biology, vol.8, issue.1, p.10, 2007.
DOI : 10.1186/gb-2007-8-1-r10

S. Jaenicke, C. Ander, T. Bekel, R. Bisdorf, M. Droge et al., Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing, PLoS ONE, vol.27, issue.900051, p.14519, 2011.
DOI : 10.1371/journal.pone.0014519.s001

M. Sommer, G. Dantas, and G. Church, Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora, Science, vol.325, issue.5944, pp.1128-1131, 2009.
DOI : 10.1126/science.1176950

E. Karsenti, Towards an ???Oceans Systems Biology???, Molecular Systems Biology, vol.8, issue.8575, pp.1-2
DOI : 10.1038/msb.2012.8
URL : http://doi.org/10.1038/msb.2012.8

B. Bloom, Space/time trade-offs in hash coding with allowable errors, Communications of the ACM, vol.13, issue.7, pp.422-426
DOI : 10.1145/362686.362692

J. Pell, A. Hintze, T. Brown, R. Canino-koning, A. Howe et al., Scaling metagenome sequence assembly with probabilistic de Bruijn graphs, Proceedings of the National Academy of Sciences, vol.109, issue.33
DOI : 10.1073/pnas.1121464109
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421212

A. Broder and M. Mitzenmacher, Network Applications of Bloom Filters: A Survey, Internet Mathematics, vol.1, issue.4, pp.485-509, 2004.
DOI : 10.1080/15427951.2004.10129096

M. Abouelhoda, S. Kurtz, and E. Ohlebusch, Replacing suffix trees with enhanced suffix arrays, Journal of Discrete Algorithms, vol.2, issue.1, pp.53-86, 2004.
DOI : 10.1016/S1570-8667(03)00065-0
URL : http://doi.org/10.1016/s1570-8667(03)00065-0

M. Vyverman, D. Baets, B. Fack, V. Dawyndt, and P. , Prospects and limitations of full-text index structures in genome analysis, Nucleic Acids Research, vol.40, issue.15, pp.1-23, 2012.
DOI : 10.1093/nar/gks408

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

D. Rusch, A. Halpern, G. Sutton, K. Heidelberg, S. Williamson et al., The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific, PLoS Biology, vol.445, issue.3, p.77, 2007.
DOI : 10.1371/journal.pbio.0050077.sd001
URL : http://doi.org/10.1371/journal.pbio.0050077