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. Uricaru, G. Rizk, V. Lacroix, E. Quillery, O. Plantard et al., Reference-free detection of isolated SNPs, Nucleic Acids Research, vol.43, issue.2, p.11, 2015.
DOI : 10.1093/nar/gku1187

URL : https://hal.archives-ouvertes.fr/hal-01083715

R. Piskol, G. Ramaswami, and J. B. Li, Reliable Identification of Genomic Variants from RNA-Seq Data, The American Journal of Human Genetics, vol.93, issue.4, pp.641-651, 2013.
DOI : 10.1016/j.ajhg.2013.08.008

J. Romiguier, P. Gayral, M. Ballenghien, A. Bernard, V. Cahais et al., Comparative population genomics in animals uncovers the determinants of genetic diversity, Nature, vol.98, issue.7526, pp.261-263, 2014.
DOI : 10.1038/nature13685

URL : https://hal.archives-ouvertes.fr/hal-01313724

S. M. Van-belleghem, D. Roelofs, J. Van-houdt, and F. Hendrickx, De novo Transcriptome Assembly and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle Pogonus chalceus (Coleoptera, Carabidae), PLoS ONE, vol.7, issue.8, p.42605, 2012.
DOI : 10.1371/journal.pone.0042605.t004

W. Li and A. Godzik, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, issue.13, pp.1658-1659, 2006.
DOI : 10.1093/bioinformatics/btl158

C. Schï-otterer, R. Tobler, R. Kofler, and V. Nolte, Sequencing pools of individuals ??? mining genome-wide polymorphism data without big funding, Nature Reviews Genetics, vol.142, issue.11, pp.749-763, 2014.
DOI : 10.1038/nmeth.2883

T. Lappalainen, M. Sammeth, M. R. Friedländer, P. A. Hoen, J. Monlong et al., Transcriptome and genome sequencing uncovers functional variation in humans, Nature, vol.447, issue.7468, pp.506-511, 2013.
DOI : 10.1371/journal.pcbi.1000770

G. R. Abecasis, A. Auton, L. D. Brooks, M. A. Depristo, R. M. Durbin et al., An integrated map of genetic variation from 1,092 human genomes, Nature, vol.491, pp.56-65, 2012.

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

P. Peterlongo, N. Schnel, N. Pisanti, M. F. Sagot, and V. Lacroix, Identifying SNPs without a Reference Genome by Comparing Raw Reads, 2010.
DOI : 10.1007/978-3-642-16321-0_14

URL : https://hal.archives-ouvertes.fr/inria-00514887

P. A. Pevzner, H. Tang, and M. S. Waterman, An Eulerian path approach to DNA fragment assembly, Proceedings of the National Academy of Sciences, vol.98, issue.17, pp.9748-9753, 2001.
DOI : 10.1073/pnas.171285098

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

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-652, 2011.
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002

R. Chikhi and G. Rizk, Space-efficient and exact de Bruijn graph representation based on a Bloom filter, Algorithms for Molecular Biology, vol.8, issue.1, p.22, 2013.
DOI : 10.1101/gr.131383.111

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, Algorit. Mol. Biol, vol.9, issue.2, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00824697

G. Sacomoto, B. Sinaimeri, C. Marchet, V. Miele, M. Sagot et al., Navigating in a Sea of Repeats in RNA-seq without Drowning, Lect. Notes Bioinformatics, vol.8701, pp.82-96, 2014.
DOI : 10.1007/978-3-662-44753-6_7

URL : https://hal.archives-ouvertes.fr/hal-01079947

H. Tilgner, D. G. Knowles, R. Johnson, C. A. Davis, S. Chakrabortty et al., Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs, Genome Research, vol.22, issue.9, pp.1616-1625, 2012.
DOI : 10.1101/gr.134445.111

W. J. Kent, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202. Article published online before March 2002

J. Lu, J. K. Tomfohr, and T. B. Kepler, Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach, BMC Bioinformatics, vol.6, issue.1, 2005.

M. D. Robinson and G. K. Smyth, Moderated statistical tests for assessing differences in tag abundance, Bioinformatics, vol.23, issue.21, pp.2881-2887, 2007.
DOI : 10.1093/bioinformatics/btm453

S. Anders, Analysing RNA-Seq data with the DESeq package, Mol. Biol, vol.43, pp.1-17, 2010.

M. Dillies, A. Rau, J. Aubert, C. Hennequet-antier, M. Jeanmougin et al., A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis, Briefings in Bioinformatics, vol.14, issue.6, pp.671-683, 2013.
DOI : 10.1093/bib/bbs046

URL : https://hal.archives-ouvertes.fr/hal-00782486

J. H. Bullard, E. Purdom, K. D. Hansen, and S. Dudoit, Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments, BMC Bioinformatics, vol.11, issue.1, p.94, 2010.
DOI : 10.1186/1471-2105-11-94

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B (Methodol, pp.289-300, 1995.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013.
DOI : 10.1093/bioinformatics/bts635

P. G. Engströmengstr¨engström, T. Steijger, B. Sipos, G. R. Grant, A. Kahles et al., Systematic evaluation of spliced alignment programs for RNA-seq data, Nature Methods, vol.27, issue.12, pp.1185-1191, 2013.
DOI : 10.1186/1471-2164-12-45

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

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.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

E. Pante, A. Rohfritsch, V. Becquet, K. Belkhir, N. Bierne et al., SNP Detection from De Novo Transcriptome Sequencing in the Bivalve Macoma balthica: Marker Development for Evolutionary Studies, PLoS ONE, vol.11, issue.433, p.52302, 2012.
DOI : 10.1371/journal.pone.0052302.s001

URL : https://hal.archives-ouvertes.fr/hal-00871859

F. Dedeine, F. Vavre, F. Fleury, B. Loppin, M. E. Hochberg et al., Removing symbiotic Wolbachia bacteria specifically inhibits oogenesis in a parasitic wasp, Proceedings of the National Academy of Sciences, vol.98, issue.11, pp.6247-6252, 2001.
DOI : 10.1073/pnas.101304298

URL : https://hal.archives-ouvertes.fr/hal-00427163

F. Dedeine, F. Vavre, D. D. Shoemaker, and M. Boulétreau, INTRA-INDIVIDUAL COEXISTENCE OF A WOLBACHIA STRAIN REQUIRED FOR HOST OOGENESIS WITH TWO STRAINS INDUCING CYTOPLASMIC INCOMPATIBILITY IN THE WASP ASOBARA TABIDA, Evolution, vol.262, issue.10, pp.2167-2174, 2004.
DOI : 10.1098/rspb.1998.0324

URL : https://hal.archives-ouvertes.fr/hal-00427570

N. Kremer, F. Dedeine, D. Charif, C. Finet, R. Allemand et al., Do variable compensatory mechanisms explain the polymorphism of the dependence phenotype in the Asobara tabida-wolbachia association? Evolution, pp.2969-2979, 2010.

N. Kremer, D. Voronin, D. Charif, P. Mavingui, B. Mollereau et al., Wolbachia Interferes with Ferritin Expression and Iron Metabolism in Insects, PLoS Pathogens, vol.14, issue.2, p.1000630, 2009.
DOI : 10.1371/journal.ppat.1000630.s001

URL : https://hal.archives-ouvertes.fr/hal-00539322

L. M. Matzkin, Population Genetics and Geographic Variation of Alcohol Dehydrogenase (Adh) Paralogs and Glucose-6-Phosphate Dehydrogenase (G6pd) in Drosophila mojavensis, Molecular Biology and Evolution, vol.21, issue.2, pp.276-285, 2004.
DOI : 10.1093/molbev/msh019

L. Reed, M. Nyboer, and T. Markow, Evolutionary relationships of Drosophila mojavensis geographic host races and their sister species Drosophila arizonae, Molecular Ecology, vol.34, issue.5, pp.1007-1022, 2007.
DOI : 10.1111/j.1365-294X.2006.02941.x

L. Modolo and E. Lerat, UrQt: an efficient software for the Unsupervised Quality trimming of NGS data, BMC Bioinformatics, vol.15, issue.10, p.137, 2015.
DOI : 10.1101/gr.4086505

T. Lappalainen, M. Sammeth, M. R. Friedländer, P. A. Hoen, J. Monlong et al., Transcriptome and genome sequencing uncovers functional variation in humans, Nature, vol.447, issue.7468, pp.506-511, 2013.
DOI : 10.1371/journal.pcbi.1000770

G. Ramaswami and J. B. Li, RADAR: a rigorously annotated database of A-to-I RNA editing, Nucleic Acids Research, vol.42, issue.D1, pp.109-113, 2014.
DOI : 10.1093/nar/gkt996

P. Cingolani, A. Platts, L. L. Wang, M. Coon, T. Nguyen et al., A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff, Fly, vol.8, issue.2, pp.80-92, 2012.
DOI : 10.1101/gr.4086505

I. A. Adzhubei, S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova et al., A method and server for predicting damaging missense mutations, Nature Methods, vol.7, issue.4, pp.248-249, 2010.
DOI : 10.1038/nmeth0410-248