G. Robertson, De novo assembly and analysis of RNA-seq data, Nature Methods, vol.7, issue.11, pp.909-912, 2010.
DOI : 10.1038/nbt0509-455

G. Sacomoto, KisSplice: de-novo calling alternative splicing events from rna-seq data, RECOMB-seq, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00784407

J. T. Simpson, ABySS: A parallel assembler for short read sequence data, Genome Research, vol.19, issue.6, pp.1117-1123, 2009.
DOI : 10.1101/gr.089532.108

P. Peterlongo, Identifying SNPs without a Reference Genome by Comparing Raw Reads, SPIRE, Springer LNCS 6393, pp.147-158, 2010.
DOI : 10.1007/978-3-642-16321-0_14

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

D. Gusfield, S. Eddhu, and C. H. Langley, OPTIMAL, EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION, Journal of Bioinformatics and Computational Biology, vol.02, issue.01, pp.173-214, 2004.
DOI : 10.1142/S0219720004000521

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, 2012.
DOI : 10.1016/0198-8859(91)90078-N

D. B. Johnson, Finding All the Elementary Circuits of a Directed Graph, SIAM Journal on Computing, vol.4, issue.1, pp.77-84, 1975.
DOI : 10.1137/0204007

P. A. Pevzner, H. Tang, and G. Tesler, De novo repeat classification and fragment assembly, RECOMB, pp.213-222, 2004.
DOI : 10.1145/974614.974643

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC515325

M. Sammeth, Complete Alternative Splicing Events Are Bubbles in Splicing Graphs, Journal of Computational Biology, vol.16, issue.8, pp.1117-1140, 2009.
DOI : 10.1089/cmb.2009.0108

R. E. Tarjan, Enumeration of the Elementary Circuits of a Directed Graph, SIAM Journal on Computing, vol.2, issue.3, pp.211-216, 1973.
DOI : 10.1137/0202017

J. C. Tiernan, An efficient search algorithm to find the elementary circuits of a graph, Communications of the ACM, vol.13, issue.12, pp.722-726, 1970.
DOI : 10.1145/362814.362819

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

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801