V. Acuña, R. Grossi, G. F. Italiano, L. Lima, R. Rizzi et al., , p.590

B. Sinaimeri, On bubble generators in directed graphs, Graph-Theoretic Concepts 591 in Computer Science -43rd International Workshop, vol.10520, pp.18-31, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01647516

C. Benoit-pilven, C. Marchet, E. Chautard, L. Lima, M. P. Lambert et al., , p.595

A. Rey, A. Cologne, S. Terrone, L. Dulaurier, J. B. Claude et al., , p.596

D. Lacroix and V. , Complementarity of assembly-first and mapping-first approaches for 597 alternative splicing annotation and differential analysis from RNAseq data, Scientific 598 Reports, vol.8, issue.1, 2018.

E. Birmelé, P. Crescenzi, R. Ferreira, R. Grossi, V. Lacroix et al., , p.600

N. Sacomoto, G. Sagot, and M. F. , Efficient Bubble Enumeration in Directed Graphs, SPIRE, pp.118-129, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00738927

B. Bollobás, Modern graph theory, Graduate Texts in Mathematics, vol.184, p.603

B. Verlag, , 1998.

L. Brankovic, C. S. Iliopoulos, R. Kundu, M. Mohamed, S. P. Pissis et al., 605 Linear-time superbubble identification algorithm for genome assembly, Computer Science, vol.606, pp.374-383, 2016.

T. H. Cormen, C. E. Leiserson, and R. L. Rivest, Introduction to Algorithms. The MIT 608

N. Deo, Graph theory with applications to engineering and computer science, p.610

, Hall series in automatic computation, 1974.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., , p.612

M. Chaisson and T. R. Gingeras, Star: ultrafast universal rna-seq aligner, Bioinformatics, vol.613, issue.1, pp.15-21, 2013.

P. M. Gleiss, J. Leydold, and P. F. Stadler, Circuit bases of strongly connected digraphs

, Discussiones Mathematicae Graph Theory, vol.23, issue.2, p.616, 2003.

Z. Iqbal, M. Caccamo, I. Turner, P. Flicek, and G. Mcvean, De novo assembly and 617 genotyping of variants using colored de bruijn graphs, Nat Genet, vol.44, issue.2, p.618, 2012.

T. Kavitha, C. Liebchen, K. Mehlhorn, D. Michail, R. Rizzi et al., , p.619

K. A. Zweig, Cycle bases in graphs characterization, algorithms, complexity, and 620 applications, Computer Science Review, vol.3, issue.4, pp.199-243, 2009.

T. Kavitha and K. Mehlhorn, Algorithms to compute minimum cycle bases in directed 623 graphs, Theory of Computing Systems, vol.40, issue.4, p.624, 2007.

L. Lima, B. Sinaimeri, G. Sacomoto, H. Lopez-maestre, C. Marchet et al., , p.625

M. F. Lacroix and V. , Playing hide and seek with repeats in local and global de novo 626 transcriptome assembly of short rna-seq reads, Algorithms Mol Biol, vol.12, issue.2, 2017.

,

S. Maclane, A combinatorial condition for planar graphs, Fundamenta Mathematicae, vol.629, issue.28, p.630, 1937.

J. R. Miller, S. Koren, and G. Sutton, Assembly algorithms for next-generation sequencing 631 data, Genomics, vol.95, issue.6, pp.315-327, 2010.

T. Onodera, K. Sadakane, and T. Shibuya, Detecting Superbubbles in Assembly Graphs

, Lecture Notes in Computer Science, vol.8126, pp.634-338, 2013.

P. A. Pevzner, H. Tang, and G. Tesler, De Novo Repeat Classification and Fragment As-636 sembly, Genome Research, vol.14, issue.9, p.637, 2004.

G. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou et al., , p.638

P. Longo and V. Lacroix, Kissplice: de-novo calling alternative splicing events from rna-seq 639 data, BMC Bioinformatics, vol.13, issue.6, p.5, 2012.

G. Sacomoto, V. Lacroix, and M. F. Sagot, A polynomial delay algorithm for the enumer-641 ation of bubbles with length constraints in directed graphs and its application to the 642 detection of alternative splicing in RNA-seq data, p.643, 2013.

M. Sammeth, Complete alternative splicing events are bubbles in splicing graphs, Computational Biology, vol.16, issue.8, p.645, 2009.

G. E. Shilov, Linear Algebra, Trans. R. A, vol.646, 1977.

. Silverman, , p.647

J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J. Jones et al., ABySS: 648 A parallel assembler for short read sequence data, Genome Research, vol.19, issue.6, pp.1117-1123

W. K. Sung, K. Sadakane, T. Shibuya, A. Belorkar, and I. Pyrogova, An O(m log m)-time 651 algorithm for detecting superbubbles, IEEE/ACM Trans. Comput. Biol. Bioinformatics, vol.652, issue.4, pp.770-777, 2015.

R. Uricaru, G. Rizk, V. Lacroix, E. Quillery, O. Plantard et al., , p.654

P. Peterlongo, Reference-free detection of isolated SNPs, Nucleic Acids Research, vol.43, issue.2, p.11, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01083715

R. Younsi and D. Maclean, Using 2k + 2 bubble searches to find single nucleotide poly-657 morphisms in k-mer graphs, Bioinformatics, vol.31, issue.5, p.658, 2015.

D. Zerbino and E. Birney, Velvet: Algorithms for De Novo Short Read Assembly Using De