T. O. Delmont, Structure, fluctuation and magnitude of a natural grassland soil metagenome, The ISME Journal, vol.64, issue.9, pp.1677-1687, 2012.
DOI : 10.1038/nrmicro2119
URL : https://hal.archives-ouvertes.fr/hal-00747243

J. Qin, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.13, issue.7285, pp.59-65, 2010.
DOI : 10.1038/nature08821
URL : https://hal.archives-ouvertes.fr/cea-00908974

E. Karsenti, A Holistic Approach to Marine Eco-Systems Biology, PLoS Biology, vol.6, issue.10, 2011.
DOI : 10.1371/journal.pbio.1001177.g002
URL : https://hal.archives-ouvertes.fr/hal-00691580

M. Pignatelli and A. Moya, Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data, PLoS ONE, vol.5, issue.5, 2011.
DOI : 10.1371/journal.pone.0019984.s008

Y. Wang, MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample, Bioinformatics, vol.28, issue.18, p.2012
DOI : 10.1093/bioinformatics/bts397

D. H. Huson, MEGAN analysis of metagenomic data, Genome Research, vol.17, issue.3, pp.377-386, 2007.
DOI : 10.1101/gr.5969107

V. M. Markowitz, IMG/M: the integrated metagenome data management and comparative analysis system, Nucleic Acids Research, vol.40, issue.D1, 2012.
DOI : 10.1093/nar/gkr975

A. M. Schnoes, Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies, PLoS Computational Biology, vol.117, issue.12, p.1000605, 2009.
DOI : 10.1371/journal.pcbi.1000605.s006

T. O. Delmont, P. Simonet, and T. M. Vogel, Describing microbial communities and performing global comparisons in the ???omic era, The ISME Journal, vol.9, issue.9, pp.1625-1628, 2012.
DOI : 10.1038/nature02340
URL : https://hal.archives-ouvertes.fr/hal-00747239

S. Jaenicke, Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing, PLoS ONE, vol.27, issue.900051, 2011.
DOI : 10.1371/journal.pone.0014519.s001

M. O. Sommer, G. Dantas, and G. M. 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

K. U. Foerstner, Environments shape the nucleotide composition of genomes, EMBO reports, vol.33, issue.12, pp.1208-1213, 2005.
DOI : 10.1126/science.1093857

J. Raes, 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

B. Jiang, Comparison of metagenomic samples using sequence signatures, BMC Genomics, vol.13, issue.1, p.730, 2012.
DOI : 10.1093/bioinformatics/btq706

W. J. Kent, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202

B. E. Dutilh, Reference-independent comparative metagenomics using cross-assembly: crAss, Bioinformatics, vol.28, issue.24, pp.3225-3123074261, 2012.
DOI : 10.1093/bioinformatics/bts613

D. Fimereli, V. Detours, and T. Konopka, TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data, Nucleic Acids Research, vol.41, issue.7, pp.1-8, 2013.
DOI : 10.1093/nar/gkt094

N. Maillet, Compareads: comparing huge metagenomic experiments, BMC Bioinformatics, vol.13, issue.Suppl 19, p.10, 2012.
DOI : 10.1371/journal.pbio.0050077
URL : https://hal.archives-ouvertes.fr/hal-00760332

B. H. Bloom, Space/time trade-offs in hash coding with allowable errors, Communications of the ACM, vol.13, issue.7, pp.422-426, 1970.
DOI : 10.1145/362686.362692

C. E. Shannon, A mathematical theory of communication, The Bell System Technical Journal, pp.379-423, 1948.

T. O. Delmont, Accessing the Soil Metagenome for Studies of Microbial Diversity, Applied and Environmental Microbiology, vol.77, issue.4, pp.1315-1324, 2011.
DOI : 10.1128/AEM.01526-10
URL : https://hal.archives-ouvertes.fr/hal-00579312

F. Meyer, The metagenomics RAST server ??? a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, vol.9, issue.1, p.386, 2008.
DOI : 10.1186/1471-2105-9-386