L. Phan, J. Hsu, M. Tri, T. Mansour, Y. Kai et al., dbvar structural variant cluster set for data analysis and variant comparison, 1000.

C. Chiang, M. Ryan, . Layer, G. Gregory, . Faust et al., Speedseq: ultra-fast personal genome analysis and interpretation, Nature methods, vol.12, issue.10, p.966, 2015.

D. Antaki, M. William, J. Brandler, and . Sebat, Sv2: accurate structural variation genotyping and de novo mutation detection from whole genomes, Bioinformatics, vol.34, issue.10, pp.1774-1777, 2017.

P. Khorsand and F. Hormozdiari, Nebula: Ultra-efficient mapping-free structural variant genotyper. bioRxiv, p.566620, 2019.

G. Bernardini, P. Bonizzoni, L. Denti, M. Previtali, and A. Schönhuth, Malva: genotyping by mapping-free allele detection of known variants, BioRxiv, p.575126, 2019.

J. Fritz, P. Sedlazeck, M. Rescheneder, H. Smolka, M. Fang et al., Accurate detection of complex structural variations using single-molecule sequencing, Nat Methods, vol.15, issue.6, pp.461-468, 2018.

M. J. Mircea-cretu-stancu, I. Van-roosmalen, M. M. Renkens, S. Nieboer, J. Middelkamp et al., Mapping and phasing of structural variation in patient genomes using nanopore sequencing, Nature communications, vol.8, issue.1, p.1326, 2017.

H. Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, vol.34, issue.18, pp.3094-3100, 2018.

K. Bianca, J. Stöcker, S. Köster, and . Rahmann, Simlord: simulation of long read data, Bioinformatics, vol.32, issue.17, pp.2704-2706, 2016.

M. Jain, S. Koren, H. Karen, J. Miga, . Quick et al., Nanopore sequencing and assembly of a human genome with ultra-long reads, Nature biotechnology, vol.36, issue.4, p.338, 2018.

M. Pendleton, R. Sebra, A. Wing-chun, A. Pang, O. Ummat et al., Assembly and diploid architecture of an individual human genome via single-molecule technologies, Nature methods, vol.12, issue.8, p.780, 2015.

A. D. Wouter-de-coster, T. D. Roeck, . Pooter, D. Svenn, P. De-rijk et al., Structural variants identified by oxford nanopore promethion sequencing of the human genome, BioRxiv, p.434118, 2018.

C. Adam, W. J. English, J. Salerno, and . Reid, Pbhoney: identifying genomic variants via long-read discordance and interrupted mapping, BMC bioinformatics, vol.15, issue.1, p.180, 2014.

J. P. Mark, J. Chaisson, . Huddleston, Y. Megan, . Dennis et al., Resolving the complexity of the human genome using single-molecule sequencing, Nature, vol.517, issue.7536, p.608, 2015.

N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, and P. Peterlongo, Compareads: comparing huge metagenomic experiments, BMC Bioinformatics, vol.13, p.10, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00720951

C. Marchet, L. Lecompte, A. Limasset, L. Bittner, and P. Peterlongo, A resourcefrugal probabilistic dictionary and applications in bioinformatics, Discrete Applied Mathematics, pp.1-11, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01873312

H. Parikh, M. Mohiyuddin, Y. K. Hugo, H. Lam, D. Iyer et al., svclassify: a method to establish benchmark structural variant calls, BMC genomics, vol.17, issue.1, p.64, 2016.

C. Daniel, C. Jeffares, M. Jolly, D. Hoti, L. Speed et al., Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast, Nature communications, vol.8, p.14061, 2017.