X. Xu, X. Liu, S. Ge, J. D. Jensen, F. Hu et al., Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes, Nature Biotechnology, vol.36, issue.1, pp.105-111, 2012.
DOI : 10.1016/0040-5809(75)90020-9

E. Quillery, O. Quenez, P. Peterlongo, and O. Plantard, : isolation and characterization of single nucleotide polymorphisms, Molecular Ecology Resources, vol.10, issue.2, pp.393-400, 2014.
DOI : 10.1111/1755-0998.12179

M. A. Depristo, E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire et al., A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nature Genetics, vol.8, issue.5, pp.43-491, 2011.
DOI : 10.1126/science.1177074

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.25-2078, 2009.
DOI : 10.1093/bioinformatics/btp352

H. Li, Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly, Bioinformatics, vol.28, issue.14, pp.1838-1844, 2012.
DOI : 10.1093/bioinformatics/bts280

E. Willing, M. Hoffmann, J. D. Klein, D. Weigel, and C. Dreyer, Paired-end RAD-seq for de novo assembly and marker design without available reference, Bioinformatics, vol.27, issue.16, pp.27-2187, 2011.
DOI : 10.1093/bioinformatics/btr346

P. Peterlongo, N. Schnel, N. Pisanti, M. Sagot, and V. Lacroix, Identifying SNPs without a Reference Genome by Comparing Raw Reads, String Processing and Information Retrieval Springer, pp.147-158, 2010.
DOI : 10.1007/978-3-642-16321-0_14
URL : https://hal.archives-ouvertes.fr/inria-00514887

Z. Iqbal, M. Caccamo, I. Turner, P. Flicek, and G. Mcvean, De novo assembly and genotyping of variants using colored de Bruijn graphs, Nature Genetics, vol.44, issue.2, pp.226-232, 2012.
DOI : 10.1016/0198-8859(91)90078-N

R. M. Leggett, R. H. Ramirez-gonzalez, W. Verweij, C. G. Kawashima, Z. Iqbal et al., Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs, PLoS ONE, vol.112, issue.25, p.60058, 2013.
DOI : 10.1371/journal.pone.0060058.s010

K. J. Nordström, M. C. Albani, G. V. James, C. Gutjahr, B. Hartwig et al., Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers, Nature Biotechnology, vol.408, issue.4, pp.31-325, 2013.
DOI : 10.1016/j.tplants.2011.02.006

G. A. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou et al., KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, BMC bioinformatics, pp.13-18, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00784407

S. N. Gardner and B. G. Hall, When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes, PLoS ONE, vol.109, issue.12, p.81760, 2013.
DOI : 10.1371/journal.pone.0081760.s004

D. R. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107

R. Chikhi and G. Rizk, Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter, WABI, pp.236-248, 2012.
DOI : 10.1007/978-3-642-33122-0_19
URL : https://hal.archives-ouvertes.fr/hal-00753930

K. Salikhov, G. Sacomoto, and G. Kucherov, Using cascading Bloom filters to improve the memory usage for de Brujin graphs, Algorithms in Bioinformatics Springer pp, pp.364-376, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00971576

K. Wong, S. Bumpstead, L. Van-der-weyden, L. G. Reinholdt, L. G. Wilming et al., Sequencing and characterization of the FVB/NJ mouse genome, Genome Biology, vol.13, issue.8, pp.13-72, 2012.
DOI : 10.1093/nar/29.1.308

D. J. Kvitek and G. Sherlock, Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment, PLoS Genetics, vol.20, issue.103, pp.9-1003972, 2013.
DOI : 10.1371/journal.pgen.1003972.s009

A. Ullmann, C. Lima, F. Guerrero, J. Piesman, and W. Black, Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus, Insect Molecular Biology, vol.3, issue.2, pp.217-222, 2005.
DOI : 10.1046/j.1365-2583.2003.00402.x

G. Rizk and D. Lavenier, GASSST: global alignment short sequence search tool, Bioinformatics, vol.26, issue.20, pp.2534-2540, 2010.
DOI : 10.1093/bioinformatics/btq485
URL : https://hal.archives-ouvertes.fr/hal-00531499

J. Wang, M. Lin, A. Crenshaw, A. Hutchinson, B. Hicks et al., High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays, BMC Genomics, vol.10, issue.1, p.561, 2009.
DOI : 10.1186/1471-2164-10-561
URL : http://doi.org/10.1186/1471-2164-10-561

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: an empirically improved memory-efficient short, p.18, 2012.
DOI : 10.1186/2047-217x-1-18
URL : http://doi.org/10.1186/2047-217x-1-18

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data, Genome Research, vol.20, issue.9, pp.1297-1303, 2010.
DOI : 10.1101/gr.107524.110

D. J. Gubler, Resurgent Vector-Borne Diseases as a Global Health Problem, Emerging infectious diseases, p.442, 1998.
DOI : 10.3201/eid0403.980326

P. Parola and D. Raoult, Tick-borne bacterial diseases emerging in Europe, Clinical Microbiology and Infection, vol.7, issue.2, pp.80-83, 2001.
DOI : 10.1046/j.1469-0691.2001.00200.x