A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, 2014.

M. Breitbart, M. Haynes, S. Kelley, F. Angly, R. A. Edwards et al., Viral diversity and dynamics in an infant gut, Research in Microbiology, vol.159, 2008.

M. Breitbart, I. Hewson, B. Felts, J. M. Mahaffy, J. Nulton et al., Metagenomic analyses of an uncultured viral community from human feces, Journal of Bacteriology, vol.185, 2003.

N. R. Coordinators, Database resources of the national center for biotechnology information, Nucleic Acids Research, vol.44, 2016.

B. E. Dutilh, N. Cassman, K. Mcnair, S. E. Sanchez, G. Silva et al., A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes, Nature Communications, vol.5, 2014.

P. Manrique, B. Bolduc, S. T. Walk, J. Van-der-oost, D. Vos et al., Healthy human gut phageome, Proceedings of the National Academy of Sciences of the United States of America, vol.113, 2016.
DOI : 10.1073/pnas.1601060113

URL : http://www.pnas.org/content/113/37/10400.full.pdf

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet Journal, vol.17, issue.1, 2011.
DOI : 10.14806/ej.17.1.200

P. J. Mcmurdie and S. Holmes, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLOS ONE, vol.8, 2013.

P. Menzel, K. L. Ng, and A. Krogh, Fast and sensitive taxonomic classification for metagenomics with Kaiju, Nature Communications, vol.7, 2016.
DOI : 10.1038/ncomms11257

URL : https://www.nature.com/articles/ncomms11257.pdf

C. Milani, S. Duranti, F. Bottacini, E. Casey, F. Turroni et al., The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota, Microbiology and Molecular Biology Reviews, vol.81, issue.4, pp.36-53, 2017.

S. Minot, A. Bryson, C. Chehoud, G. D. Wu, J. D. Lewis et al., NCBI Resource Coordinators. 2018. Database resources of the national center for biotechnology information, Proceedings of the National Academy of Sciences of the United States of America, vol.110, 2013.

J. M. Norman, S. A. Handley, M. T. Baldridge, L. Droit, C. Y. Liu et al., Disease-specific alterations in the enteric virome in inflammatory bowel disease, Cell, vol.160, 2015.

S. Nurk, D. Meleshko, A. Korobeynikov, and P. A. Pevzner, metaSPAdes: a new versatile metagenomic assembler, vol.27, 2017.
DOI : 10.1101/gr.213959.116

URL : http://europepmc.org/articles/pmc5411777?pdf=render

J. Oksanen, F. G. Blanchet, R. Kindt, P. Legendre, R. G. O'hara et al., The vegan package. Community ecology package, p.9, 2007.

. R-core-team, R: A language and environment for statistical computing, 2016.

A. Reyes, L. V. Blanton, S. Cao, G. Zhao, M. Manary et al., Gut DNA viromes of Malawian twins discordant for severe acute malnutrition, Proceedings of the National Academy of Sciences of the United States of America, vol.112, 2015.

J. M. Rodriguez, K. Murphy, C. Stanton, R. P. Ross, O. I. Kober et al., The composition of the gut microbiota throughout life, with an emphasis on early life, Microbial Ecology in Health and Disease, vol.26, p.26050, 2015.

S. Roux, F. Enault, B. L. Hurwitz, and M. B. Sullivan, VirSorter: mining viral signal from, 2015.
DOI : 10.7717/peerj.985

URL : https://hal.archives-ouvertes.fr/hal-01557667