F. Stephen, W. Altschul, W. Gish, . Miller, W. Eugene et al., Basic local alignment search tool, Journal of molecular biology, vol.215, issue.3, pp.403-410, 1990.

A. S. Amend, K. A. Seifert, and T. D. Bruns, Quantifying microbial communities with 454 pyrosequencing: does read abundance count?, Molecular Ecology, vol.59, issue.24, pp.5555-5565, 2010.
DOI : 10.1111/j.1365-294X.2010.04898.x

H. J. Atkinson, J. H. Morris, T. E. Ferrin, and P. C. Babbitt, Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies, PLoS ONE, vol.28, issue.69, p.4345, 2009.
DOI : 10.1371/journal.pone.0004345.s010

E. Bapteste, C. Bicep, and P. Lopez, Evolution of genetic diversity using networks: the human gut microbiome as a case study, Clinical Microbiology and Infection, vol.18, issue.4, pp.40-43, 2012.
DOI : 10.1111/j.1469-0691.2012.03856.x

D. Belazzougui, P. Boldi, G. Ottaviano, R. Venturini, and S. Vigna, Cache-Oblivious Peeling of Random Hypergraphs, 2014 Data Compression Conference, pp.352-361, 2014.
DOI : 10.1109/DCC.2014.48

D. Belazzougui and R. Venturini, Compressed static functions with applications to other dictionary problems\ vspace, 2012.

G. Benoit, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath et al., Figure S6: Results of Simka on low covered samples from the Global Ocean Sampling project (GOS), PeerJ Computer Science, vol.5, issue.3, pp.1-17, 2016.
DOI : 10.7717/peerj-cs.94/supp-8

E. Boon, S. Halary, E. Bapteste, and M. Hijri, Studying Genome Heterogeneity within the Arbuscular Mycorrhizal Fungal Cytoplasm, Genome Biology and Evolution, vol.7, issue.2, pp.505-521, 2015.
DOI : 10.1093/gbe/evv002
URL : https://hal.archives-ouvertes.fr/hal-01224215

D. Charles and K. Chellapilla, Bloomier Filters: A Second Look, In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics LNCS, vol.5193, pp.259-270, 2008.
DOI : 10.1007/978-3-540-87744-8_22

E. Corel, P. Lopez, R. Meheust, and E. Bapteste, Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution, Trends in Microbiology, vol.24, issue.3, pp.224-237, 2016.
DOI : 10.1016/j.tim.2015.12.003
URL : https://hal.archives-ouvertes.fr/hal-01300043

B. Veronika, . Dubinkina, S. Dmitry, . Ischenko, I. Vladimir et al., Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis, BMC Bioinformatics, vol.17, issue.1, p.38, 2016.

P. Ferragina and G. Manzini, Indexing compressed text, Journal of the ACM, vol.52, issue.4, pp.552-581, 2000.
DOI : 10.1145/1082036.1082039

M. Fondi, . Karkman, . Tamminen, . Bosi, . Virta et al., ???Every Gene Is Everywhere but the Environment Selects???: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis, Genome Biology and Evolution, vol.8, issue.5, 2016.
DOI : 10.1093/gbe/evw077

D. Forster, L. Bittner, S. Karkar, M. Dunthorn, S. Romac et al., Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms, BMC Biology, vol.163, issue.1, p.16, 2015.
DOI : 10.1186/s12915-015-0125-5
URL : https://hal.archives-ouvertes.fr/hal-01144173

G. Manfred, . Grabherr, J. Brian, M. Haas, . Yassour et al., Qiandong Zeng, et al. Full-length transcriptome assembly from rna-seq data without a reference genome, Nature biotechnology, issue.7, pp.29644-652, 2011.

R. Finstad, B. C. Amundson, J. F. Thomas, and . Banfield, A new view of the tree of life, Nature Microbiology, vol.1, p.16048, 2016.

W. Steven, M. Kembel, J. A. Wu, J. L. Eisen, and . Green, Incorporating 16s gene copy number information improves estimates of microbial diversity and abundance, PLoS Comput Biol, vol.8, issue.10, pp.1-11

A. Kirsch and M. Mitzenmacher, Less hashing, same performance: Building a better bloom filter, Algorithms?ESA 2006, pp.456-467, 2006.

V. Kunin, A. Engelbrektson, H. Ochman, and P. Hugenholtz, Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates, Environmental Microbiology, vol.64, issue.1, pp.118-123, 2010.
DOI : 10.1111/j.1462-2920.2009.02051.x

B. Langmead, L. Steven, and . Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009.
DOI : 10.1093/bioinformatics/btp324

P. Lopez, S. Halary, and E. Bapteste, Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life, Biology Direct, vol.59, issue.3, p.64, 2015.
DOI : 10.1186/s13062-015-0092-3
URL : https://hal.archives-ouvertes.fr/hal-01257771

N. Maillet, G. Collet, T. Vannier, D. Lavenier, and P. Peterlongo, Commet: Comparing and combining multiple metagenomic datasets, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.94-98, 2014.
DOI : 10.1109/BIBM.2014.6999135
URL : https://hal.archives-ouvertes.fr/hal-01080050

N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, and P. Peterlongo, Compareads: comparing huge metagenomic experiments, BMC Bioinformatics, vol.13, issue.Suppl 19, pp.1-10, 2012.
DOI : 10.1371/journal.pbio.0050077
URL : https://hal.archives-ouvertes.fr/hal-00760332

G. Marsaglia, Xorshift RNGs, Journal of Statistical Software, vol.8, issue.14, pp.1-6, 2003.
DOI : 10.18637/jss.v008.i14

G. Rizk, D. Lavenier, and R. Chikhi, DSK: k-mer counting with very low memory usage, Bioinformatics, vol.29, issue.5, pp.652-653, 2013.
DOI : 10.1093/bioinformatics/btt020
URL : https://hal.archives-ouvertes.fr/hal-00778473

G. Robertson, J. Schein, R. Chiu, R. Corbett, M. Field et al., De novo assembly and analysis of RNA-seq data, Nature Methods, vol.7, issue.11, pp.909-912, 2010.
DOI : 10.1038/nbt0509-455

M. Schirmer, U. Z. Ijaz, R. D. Amore, N. Hall, W. T. Sloan et al., Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform, Nucleic Acids Research, vol.43, issue.6, 2015.
DOI : 10.1093/nar/gku1341

C. Stephan and . Schuster, Next-generation sequencing transforms todays biology, Nature, vol.200, issue.8, pp.16-18, 2007.

D. Sharon, H. Tilgner, F. Grubert, and M. Snyder, A singlemolecule long-read survey of the human transcriptome, Nature biotechnology, issue.11, pp.311009-1014, 2013.

H. Tilgner, F. Grubert, D. Sharon, P. Michael, and . Snyder, Defining a personal, allele-specific, and single-molecule long-read transcriptome, Proceedings of the National Academy of Sciences, vol.111, issue.27, pp.9869-9874, 2014.
DOI : 10.1073/pnas.1400447111

F. Völkel, E. Bapteste, M. Habib, P. Lopez, and C. Vigliotti, Read networks and k-laminar graphs. working paper or preprint, 2016.

E. Zorita, P. Cuscó, and G. J. Filion, Starcode: sequence clustering based on all-pairs search, Bioinformatics, vol.31, issue.12, pp.311913-1919, 2015.
DOI : 10.1093/bioinformatics/btv053