M. Almeida, A. Hébert, A. L. Abraham, S. Rasmussen, C. Monnet et al., Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products, BMC genomics, vol.13, issue.1, p.1101, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01195502

N. Segata, L. Waldron, A. Ballarini, V. Narasimhan, O. Jousson et al., Metagenomic microbial community profiling using unique clade-specific marker genes, Nature methods, vol.1, issue.8, pp.811-815, 2012.

B. Liu, T. Gibbons, M. Ghodsi, M. Pop, and . Metaphyler, Taxonomic profiling for metagenomic sequences. InBioinformatics and Biomedicine (BIBM), pp.95-100, 2010.

S. Sunagawa, D. R. Mende, G. Zeller, F. Izquierdo-carrasco, S. A. Berger et al., Metagenomic species profiling using universal phylogenetic marker genes, Nature methods, vol.10, issue.12, pp.1196-1205, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01204281

R. Ounit, S. Wanamaker, T. J. Close, and L. S. Clark, fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers, BMC genomics, vol.25, issue.1, p.236, 2015.

D. E. Wood and S. L. Salzberg, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome biology, vol.15, issue.3, p.46, 2014.

S. K. Ames, D. A. Hysom, S. N. Gardner, G. S. Lloyd, M. B. Gokhale et al., Scalable metagenomic taxonomy classification using a reference genome database, Bioinformatics, vol.15, issue.18, pp.2253-60, 2013.

S. S. Minot, N. Krumm, and N. B. Greenfield, One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification, p.27607, 2015.

C. F. Davenport, J. Neugebauer, N. Beckmann, B. Friedrich, B. Kameri et al., Genometa-a fast and accurate classifier for short metagenomic shotgun reads, PloS one, vol.21, issue.8, p.41224, 2012.

T. A. Freitas, P. E. Li, M. B. Scholz, and P. S. Chain, Accurate read-based metagenome characterization using a hierarchical suite of unique signatures, Nucleic acids research, vol.12, p.180, 2015.

D. H. Huson, A. F. Auch, J. Qi, and S. C. Schuster, MEGAN analysis of metagenomic data, Genome research, vol.1, issue.3, pp.377-86, 2007.

M. S. Lindner and R. By, Metagenomic profiling of known and unknown microbes with MicrobeGPS, PloS one, vol.10, issue.2, p.117711, 2015.

T. H. Ahn, J. Chai, and C. Pan, Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance, Bioinformatics, vol.29, p.641, 2014.

S. Hunter, M. Corbett, H. Denise, M. Fraser, A. Gonzalez-beltran et al., EBI metagenomics-a new resource for the analysis and archiving of metagenomic data, Nucleic acids research, vol.1, issue.D1, pp.600-606, 2014.

F. Meyer, D. Paarmann, D. Souza, M. Olson, R. Glass et al., The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC bioinformatics, vol.19, issue.1, p.386, 2008.

R. Bossy, W. Golik, Z. Ratkovic, P. Bessières, and C. Nédellec, Bionlp shared task 2013-an overview of the bacteria biotope task. InProceedings of the BioNLP Shared Task, pp.161-169, 2013.

P. Yilmaz, R. Kottmann, D. Field, R. Knight, J. R. Cole et al., Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications, Nature biotechnology, vol.1, issue.5, pp.415-435, 2011.

J. Goecks, A. Nekrutenko, and J. Taylor, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome biology, vol.25, issue.8, p.86, 2010.

C. Sloggett, N. Goonasekera, and E. Afgan, BioBlend: automating pipeline analyses within Galaxy and CloudMan, Bioinformatics, vol.29, issue.1, pp.1685-1691, 2013.