S. E. Abdel-ghany, M. Hamilton, J. L. Jacobi, P. Ngam, N. Devitt et al., A survey of the sorghum transcriptome using single-molecule long reads, Nature communications, vol.7, p.11706, 2016.

B. Adamcsek, G. Palla, I. J. Farkas, I. Derényi, and T. Vicsek, Cfinder: locating cliques and overlapping modules in biological networks, Bioinformatics, vol.22, issue.8, pp.1021-1023, 2006.

B. Alberts, Molecular biology of the cell, 2017.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of molecular biology, vol.215, issue.3, pp.403-410, 1990.

S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang et al., genome-to-phenome with faang, the functional annotation of animal genomes project, Genome biology, vol.16, issue.1, p.57

K. F. Au, V. Sebastiano, P. T. Afshar, J. D. Durruthy, L. Lee et al., Characterization of the human esc transcriptome by hybrid sequencing, Proceedings of the National Academy of Sciences, vol.110, issue.50, pp.4821-4830, 2013.

S. Balzano, E. Corre, J. Decelle, R. Sierra, P. Wincker et al., Transcriptome analyses to investigate symbiotic relationships between marine protists, Frontiers in microbiology, vol.6, p.98, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01143962

E. Bao, T. Jiang, I. Kaloshian, G. , and T. , Seed: efficient clustering of next-generation sequences, Bioinformatics, vol.27, issue.18, pp.2502-2509, 2011.

E. Bao and L. Lan, Halc: High throughput algorithm for long read error correction, BMC bioinformatics, vol.18, issue.1, p.204, 2017.

Y. Barash, J. A. Calarco, W. Gao, Q. Pan, X. Wang et al., Deciphering the splicing code, Nature, vol.465, issue.7294, p.53, 2010.

M. Bastide and W. R. Mccombie, Assembling genomic dna sequences with phrap, Current Protocols in Bioinformatics, pp.11-15, 2007.

Y. Benjamini and T. P. Speed, Summarizing and correcting the gc content bias in highthroughput sequencing, Nucleic acids research, vol.40, issue.10, pp.72-72, 2012.

G. Benoit, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath et al., Multiple Comparative Metagenomics using Multiset k-mer Counting, pp.1-17, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01397150

C. Benoit-pilven, C. Marchet, E. Chautard, L. Lima, M. Lambert et al., Complementarity of assembly-first and mappingfirst approaches for alternative splicing annotation and differential analysis from rnaseq data, Scientific reports, vol.8, issue.1, p.4307, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01924204

S. M. Berget, C. Moore, and P. A. Sharp, Spliced segments at the 5 ´ terminus of adenovirus 2 late mrna, Proceedings of the National Academy of Sciences, vol.74, issue.8, pp.3171-3175, 1977.

K. Berlin, S. Koren, C. Chin, J. P. Drake, J. M. Landolin et al., Assembling large genomes with single-molecule sequencing and locality-sensitive hashing, Nature biotechnology, vol.33, issue.6, pp.623-630, 2015.

K. Berlin, S. Koren, C. Chin, J. P. Drake, J. M. Landolin et al., Assembling large genomes with single-molecule sequencing and locality-sensitive hashing, Nature biotechnology, vol.33, issue.6, pp.623-630, 2015.

T. Biard, L. Pillet, J. Decelle, C. Poirier, N. Suzuki et al., Towards an integrative morpho-molecular classification of the collodaria (polycystinea, radiolaria), Protist, vol.166, issue.3, pp.374-388, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01253985

V. D. Blondel, J. Guillaume, R. Lambiotte, and E. Lefebvre, Fast unfolding of communities in large networks, Journal of statistical mechanics: theory and experiment, issue.10, p.10008, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01146070

M. T. Bolisetty, G. Rajadinakaran, and B. R. Graveley, Determining exon connectivity in complex mrnas by nanopore sequencing, Genome biology, vol.16, issue.1, p.204, 2015.

P. Bork, C. Bowler, C. De-vargas, G. Gorsky, E. Karsenti et al., Tara oceans studies plankton at planetary scale, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01258211

J. Bouck, W. Yu, R. Gibbs, and K. Worley, Comparison of gene indexing databases, Trends in Genetics, vol.15, issue.4, pp.159-162, 1999.

N. L. Bray, H. Pimentel, P. Melsted, and L. Pachter, Near-optimal probabilistic rna-seq quantification, Nature biotechnology, vol.34, issue.5, p.525, 2016.

J. Burke, D. Davison, and W. Hide, d2 cluster: a validated method for clustering est and full-length cdna sequences, Genome research, vol.9, issue.11, pp.1135-1142, 1999.

J. Burke, D. Davison, and W. Hide, d2 cluster: a validated method for clustering est and full-length cdna sequences, Genome research, vol.9, issue.11, pp.1135-1142, 1999.

A. Byrne, A. E. Beaudin, H. E. Olsen, M. Jain, C. Cole et al., Nanopore long-read rnaseq reveals widespread transcriptional variation among the surface receptors of individual b cells, Nature Communications, vol.8, p.16027, 2017.

M. O. Carneiro, C. Russ, M. G. Ross, S. B. Gabriel, C. Nusbaum et al., Pacific biosciences sequencing technology for genotyping and variation discovery in human data, BMC genomics, vol.13, issue.1, p.375, 2012.

A. B. Carvalho, E. G. Dupim, and G. Goldstein, Improved assembly of noisy long reads by k-mer validation, Genome Research, vol.26, issue.12, pp.1710-1720, 2016.

E. Chacko and S. Ranganathan, Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse, BMC genomics, vol.10, issue.1, p.5, 2009.

M. J. Chaisson and G. Tesler, Mapping single molecule sequencing reads using basic local alignment with successive refinement (blasr): application and theory, BMC bioinformatics, vol.13, issue.1, p.238, 2012.

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.22, p.1, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00753930

C. Chin, D. H. Alexander, P. Marks, A. A. Klammer, J. Drake et al., Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data, Nature methods, vol.10, issue.6, pp.563-569, 2013.

C. Chin, P. Peluso, F. J. Sedlazeck, M. Nattestad, G. T. Concepcion et al., Phased diploid genome assembly with single-molecule real-time sequencing, Nature methods, vol.13, issue.12, p.1050, 2016.

Z. Chong, J. Ruan, and C. Wu, Rainbow: an integrated tool for efficient clustering and assembling rad-seq reads, Bioinformatics, vol.28, issue.21, pp.2732-2737, 2012.

A. Christoffels, A. Van-gelder, G. Greyling, R. Miller, T. Hide et al., Stack: sequence tag alignment and consensus knowledgebase, Nucleic Acids Research, vol.29, issue.1, pp.234-238, 2001.

J. Chu, H. Mohamadi, R. L. Warren, C. Yang, and I. Birol, Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art, Bioinformatics, vol.33, issue.8, pp.1261-1270, 2016.

A. Clauset, M. E. Newman, M. , and C. , Finding community structure in very large networks, Physical review E, vol.70, issue.6, p.66111, 2004.

P. J. Cock, C. J. Fields, N. Goto, M. L. Heuer, R. et al., The sanger fastq file format for sequences with quality scores, and the solexa/illumina fastq variants, Nucleic acids research, vol.38, issue.6, pp.1767-1771, 2009.

W. Commons, File:difference dna rna-en.svg-wikimedia commons, the free media repository, 2018.

E. P. Consortium, The encode (encyclopedia of dna elements) project, Science, vol.306, issue.5696, pp.636-640, 2004.

E. P. Consortium, Identification and analysis of functional elements in 1% of the human genome by the encode pilot project, nature, vol.447, issue.7146, p.799, 2007.

T. H. Cormen, Introduction to algorithms, 2009.

B. P. Cusack, P. F. Arndt, L. Duret, C. , and H. R. , Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes, PLoS genetics, vol.7, issue.10, p.1002276, 2011.
URL : https://hal.archives-ouvertes.fr/inserm-00711772

E. Dahlhaus, D. S. Johnson, C. H. Papadimitriou, P. D. Seymour, Y. et al., The complexity of multiterminal cuts, SIAM Journal on Computing, vol.23, issue.4, pp.864-894, 1994.

M. David, M. Dzamba, D. Lister, L. Ilie, and M. Brudno, Shrimp2: sensitive yet practical short read mapping, Bioinformatics, vol.27, issue.7, pp.1011-1012, 2011.

S. K. Davy, D. Allemand, and V. M. Weis, Cell biology of cnidarian-dinoflagellate symbiosis, Microbiology and Molecular Biology Reviews, vol.76, issue.2, pp.229-261, 2012.

C. De-lannoy, D. De-ridder, R. , and J. , The long reads ahead: de novo genome assembly using the minion, 2017.

A. L. Delcher, S. Kasif, R. D. Fleischmann, J. Peterson, O. White et al., Alignment of whole genomes, Nucleic acids research, vol.27, issue.11, pp.2369-2376, 1999.

S. Djebali, C. A. Davis, A. Merkel, A. Dobin, T. Lassmann et al., Landscape of transcription in human cells, Nature, vol.489, issue.7414, p.101, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01216755

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.

B. Dost, C. Wu, A. Su, and V. Bafna, Tclust: A fast method for clustering genome-scale expression data, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol.8, issue.3, pp.808-818, 2011.

E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre et al., Gatb: Genome assembly & analysis tool box, Bioinformatics, vol.30, issue.20, pp.2959-2961, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01088571

J. Eckmann and E. Moses, Curvature of co-links uncovers hidden thematic layers in the world wide web, Proceedings of the national academy of sciences, vol.99, pp.5825-5829, 2002.

P. Edery, C. Marcaillou, M. Sahbatou, A. Labalme, J. Chastang et al., Association of tals developmental disorder with defect in minor splicing component u4atac snrna, Science, vol.332, issue.6026, pp.240-243, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01017145

R. C. Edgar, Search and clustering orders of magnitude faster than blast, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.

M. Escalona, S. Rocha, and D. Posada, A comparison of tools for the simulation of genomic next-generation sequencing data, Nature Reviews Genetics, vol.17, issue.8, p.459, 2016.

, Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, 2008.

D. Feng and R. F. Doolittle, Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships, Journal of molecular evolution, vol.44, issue.4, pp.361-370, 1997.

E. B. Fichot and R. S. Norman, Microbial phylogenetic profiling with the pacific biosciences sequencing platform, vol.1, p.10, 2013.

C. L. Fiore, M. Labrie, J. K. Jarett, and M. P. Lesser, Transcriptional activity of the giant barrel sponge, xestospongia muta holobiont: molecular evidence for metabolic interchange, Frontiers in microbiology, vol.6, p.364, 2015.

S. Foissac and M. Sammeth, Astalavista: dynamic and flexible analysis of alternative splicing events in custom gene datasets, Nucleic acids research, vol.35, issue.2, pp.297-299, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01588027

D. Forster, L. Bittner, S. Karkar, M. Dunthorn, S. Romac et al., Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms, BMC biology, vol.13, issue.1, p.16, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01144173

S. Fortunato, Community detection in graphs, Physics reports, vol.486, issue.3-5, pp.75-174, 2010.

S. Fortunato and M. Barthelemy, Resolution limit in community detection, Proceedings of the National Academy of Sciences, vol.104, issue.1, pp.36-41, 2007.

S. Fortunato, V. Latora, and M. Marchiori, Method to find community structures based on information centrality, Physical review E, vol.70, issue.5, p.56104, 2004.

K. J. Friedman, J. Kole, J. A. Cohn, M. R. Knowles, L. M. Silverman et al., Correction of aberrant splicing of the cystic fibrosis transmembrane conductance regulator (cftr) gene by antisense oligonucleotides, Journal of Biological Chemistry, vol.274, issue.51, pp.36193-36199, 1999.

N. J. Fuda, M. B. Ardehali, and J. T. Lis, Defining mechanisms that regulate rna polymerase ii transcription in vivo, Nature, vol.461, issue.7261, p.186, 2009.

J. Gauthier, C. Mouden, T. Suchan, N. Alvarez, N. Arrigo et al., Discosnp-rad: de novo detection of small variants for population genomics. bioRxiv, p.216747, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01634232

M. Ghodsi, B. Liu, and M. Pop, Dnaclust: accurate and efficient clustering of phylogenetic marker genes, BMC bioinformatics, vol.12, issue.1, p.271, 2011.

M. Girvan and M. E. Newman, Community structure in social and biological networks, Proceedings of the national academy of sciences, vol.99, pp.7821-7826, 2002.

M. Girvan and M. E. Newman, Community structure in social and biological networks, Proceedings of the national academy of sciences, vol.99, pp.7821-7826, 2002.

M. L. Gonzalez-garay, Introduction to isoform sequencing using pacific biosciences technology (iso-seq), Transcriptomics and Gene Regulation, pp.141-160, 2016.

B. H. Good, Y. De-montjoye, C. , and A. , Performance of modularity maximization in practical contexts, Physical Review E, vol.81, issue.4, p.46106, 2010.

S. Goodwin, J. Gurtowski, S. Ethe-sayers, P. Deshpande, M. C. Schatz et al., Oxford nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome, Genome research, vol.25, issue.11, pp.1750-1756, 2015.

S. P. Gordon, E. Tseng, A. Salamov, J. Zhang, X. Meng et al., Widespread polycistronic transcripts in fungi revealed by single-molecule mrna sequencing, PloS one, vol.10, issue.7, p.132628, 2015.

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.29, issue.7, pp.644-652, 2011.

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., Trinity: reconstructing a full-length transcriptome without a genome from rna-seq data, Nature biotechnology, vol.29, issue.7, p.644, 2011.

G. R. Grant, M. H. Farkas, A. D. Pizarro, N. F. Lahens, J. Schug et al., Comparative analysis of rna-seq alignment algorithms and the rna-seq unified mapper (rum), Bioinformatics, issue.18, pp.2518-2528, 2011.

T. Griebel, B. Zacher, P. Ribeca, E. Raineri, V. Lacroix et al., Modelling and simulating generic rna-seq experiments with the flux simulator, Nucleic acids research, vol.40, issue.20, pp.10073-10083, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00744755

L. Guidi, S. Chaffron, L. Bittner, D. Eveillard, A. Larhlimi et al., Plankton networks driving carbon export in the oligotrophic ocean, Nature, vol.532, issue.7600, p.465, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01275276

S. K. Gupta, J. D. Kececioglu, and A. A. Schäffer, Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment, Journal of Computational Biology, vol.2, issue.3, pp.459-472, 1995.

T. Hackl, R. Hedrich, J. Schultz, and F. Förster, proovread: large-scale high-accuracy pacbio correction through iterative short read consensus, Bioinformatics, vol.30, issue.21, pp.3004-3011, 2014.

E. Haghshenas, F. Hach, S. C. Sahinalp, C. , and C. , Colormap: Correcting long reads by mapping short reads, Bioinformatics, vol.32, issue.17, pp.545-551, 2016.

S. Heber, M. Alekseyev, S. Sze, H. Tang, and P. A. Pevzner, Splicing graphs and est assembly problem, Bioinformatics, vol.18, issue.1, pp.181-188, 2002.

U. Hentschel, K. M. Usher, T. , and M. W. , Marine sponges as microbial fermenters, FEMS microbiology ecology, vol.55, issue.2, pp.167-177, 2006.

D. G. Higgins and P. M. Sharp, Clustal: a package for performing multiple sequence alignment on a microcomputer, Gene, vol.73, issue.1, pp.237-244, 1988.

N. V. Hoang, A. Furtado, P. J. Mason, A. Marquardt, L. Kasirajan et al., A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing, BMC genomics, vol.18, issue.1, p.395, 2017.

O. Hoegh-guldberg, Climate change, coral bleaching and the future of the world's coral reefs. Marine and freshwater research, vol.50, pp.839-866, 1999.

N. S. Holter, M. Mitra, A. Maritan, M. Cieplak, J. R. Banavar et al., Fundamental patterns underlying gene expression profiles: simplicity from complexity, Proceedings of the National Academy of Sciences, vol.97, issue.15, pp.8409-8414, 2000.

J. Hopcroft and R. Tarjan, Algorithm 447: efficient algorithms for graph manipulation, Communications of the ACM, vol.16, issue.6, pp.372-378, 1973.

W. Huang, L. Li, J. R. Myers, M. , and G. T. , Art: a next-generation sequencing read simulator, Bioinformatics, vol.28, issue.4, pp.593-594, 2011.

X. Huang and A. Madan, Cap3: A dna sequence assembly program, Genome research, vol.9, issue.9, pp.868-877, 1999.

D. H. Huson, A. F. Auch, J. Qi, and S. C. Schuster, Megan analysis of metagenomic data, Genome research, vol.17, issue.3, pp.377-386, 2007.

M. Jain, I. T. Fiddes, K. H. Miga, H. E. Olsen, B. Paten et al., Improved data analysis for the minion nanopore sequencer, Nature methods, vol.12, issue.4, p.351, 2015.

H. Jiang, Z. Ling, Y. Zhang, H. Mao, Z. Ma et al., Altered fecal microbiota composition in patients with major depressive disorder, Brain, behavior, and immunity, vol.48, pp.186-194, 2015.

P. F. Jonsson, T. Cavanna, D. Zicha, and P. A. Bates, Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis, BMC bioinformatics, vol.7, issue.1, p.2, 2006.

A. B. Kahn, Topological sorting of large networks, Communications of the ACM, vol.5, issue.11, pp.558-562, 1962.

E. Karsenti, S. G. Acinas, P. Bork, C. Bowler, C. De-vargas et al., A holistic approach to marine Eco-systems biology, PLoS Biology, p.9, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00691580

Y. Katz, E. T. Wang, E. M. Airoldi, and C. B. Burge, Analysis and design of RNA sequencing experiments for identifying isoform regulation, Nature methods, vol.7, issue.12, pp.1009-1015, 2010.

P. J. Keeling, F. Burki, H. M. Wilcox, B. Allam, E. E. Allen et al., The marine microbial eukaryote transcriptome sequencing project (mmetsp): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing, PLoS Biology, vol.12, issue.6, p.1001889, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01109521

W. J. Kent, Blat-the blast-like alignment tool, Genome research, vol.12, issue.4, pp.656-664, 2002.

N. Khiste and L. Ilie, Hisea: Hierarchical seed aligner for pacbio data, BMC Bioinformatics, vol.18, issue.1, p.564, 2017.

S. M. Kiee-lbasa, R. Wan, K. Sato, P. Horton, and M. C. Frith, Adaptive seeds tame genomic sequence comparison, Genome research, vol.21, issue.3, pp.487-493, 2011.

D. Kim, B. Langmead, and S. L. Salzberg, Hisat: a fast spliced aligner with low memory requirements, Nature methods, vol.12, issue.4, p.357, 2015.

A. Kirsch and M. Mitzenmacher, Less hashing, same performance: building a better bloom filter, European Symposium on Algorithms, pp.456-467, 2006.

S. Koren, M. C. Schatz, B. P. Walenz, J. Martin, J. T. Howard et al., Hybrid error correction and de novo assembly of single-molecule sequencing reads, Nature biotechnology, vol.30, issue.7, p.693, 2012.

S. Koren, B. P. Walenz, K. Berlin, J. R. Miller, N. H. Bergman et al., Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation, Genome research, vol.27, issue.5, pp.722-736, 2017.

A. R. Kornblihtt, I. E. Schor, M. Alló, G. Dujardin, E. Petrillo et al., Alternative splicing: a pivotal step between eukaryotic transcription and translation, Nature reviews Molecular cell biology, vol.14, issue.3, p.153, 2013.

K. Krizanovic, A. Echchiki, J. Roux, M. Sikic, A. Morales-rozo et al., Evaluation of tools for long read rna-seq splice-aware alignment, Bioinformatics, vol.1, p.7, 2017.

J. N. Kuehner, E. L. Pearson, M. , and C. , Unravelling the means to an end: Rna polymerase ii transcription termination, Nature reviews Molecular cell biology, vol.12, issue.5, p.283, 2011.

S. Kurtz, Reducing the space requirement of suffix trees. Software-Practice and Experience, vol.29, pp.1149-71, 1999.

S. La, E. Haghshenas, C. , and C. , Lrcstats, a tool for evaluating long reads correction methods, Bioinformatics, vol.33, issue.22, pp.3652-3654, 2017.

A. Lancichinetti, S. Fortunato, R. , and F. , Benchmark graphs for testing community detection algorithms, Physical review E, vol.78, issue.4, p.46110, 2008.

B. Langmead, Aligning short sequencing reads with bowtie, Current protocols in bioinformatics, pp.11-18, 2010.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with bowtie 2, Nature methods, vol.9, issue.4, p.357, 2012.

T. Lappalainen, M. Sammeth, M. R. Friedländer, P. Ac't-hoen, J. Monlong et al., Transcriptome and genome sequencing uncovers functional variation in humans, Nature, vol.501, issue.7468, p.506, 2013.

L. Bras, Y. Collin, O. Monjeaud, C. Lacroix, V. Rivals et al., Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw ngs reads, vol.5, p.9, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01280238

C. Lee, Generating consensus sequences from partial order multiple sequence alignment graphs, Bioinformatics, vol.19, issue.8, pp.999-1008, 2003.

C. Lee, C. Grasso, and M. F. Sharlow, Multiple sequence alignment using partial order graphs, Bioinformatics, vol.18, issue.3, pp.452-464, 2002.

B. Li and C. N. Dewey, Rsem: accurate transcript quantification from rna-seq data with or without a reference genome, BMC bioinformatics, vol.12, issue.1, p.323, 2011.

B. Li, N. Fillmore, Y. Bai, M. Collins, J. A. Thomson et al., Evaluation of de novo transcriptome assemblies from rna-seq data, Genome biology, vol.15, issue.12, p.553, 2014.

F. Li, C. Jiang, K. W. Krausz, Y. Li, I. Albert et al., Microbiome remodelling leads to inhibition of intestinal farnesoid x receptor signalling and decreased obesity, Nature communications, vol.4, p.2384, 2013.

H. Li, Aligning sequence reads, clone sequences and assembly contigs with bwa-mem, 2013.

H. Li, Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences, Bioinformatics, vol.32, issue.14, pp.2103-2110, 2016.

H. Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, vol.1, p.7, 2018.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009.

H. Li and R. Durbin, Fast and accurate long-read alignment with burrows-wheeler transform, Bioinformatics, vol.26, issue.5, pp.589-595, 2010.

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.

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.

L. Lima, B. Sinaimeri, G. Sacomoto, H. Lopez-maestre, C. Marchet et al., Playing hide and seek with repeats in local and global de novo transcriptome assembly of short rna-seq reads, Algorithms for molecular biology, vol.12, issue.1, p.2, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01474524

A. Limasset, J. Flot, P. , and P. , Toward perfect reads: self-correction of short reads via mapping on de bruijn graphs, RECOMB-seq, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01644163

A. Limasset, G. Rizk, R. Chikhi, P. , and P. , Fast and scalable minimal perfect hashing for massive key sets, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01566246

D. J. Lipman, S. F. Altschul, and J. D. Kececioglu, A tool for multiple sequence alignment, Proceedings of the National Academy of Sciences, vol.86, issue.12, pp.4412-4415, 1989.

Y. Liu, J. Schröder, and B. Schmidt, Musket: a multistage k-mer spectrum-based error corrector for illumina sequence data, Bioinformatics, vol.29, issue.3, pp.308-315, 2012.

N. J. Loman, J. Quick, and J. T. Simpson, A complete bacterial genome assembled de novo using only nanopore sequencing data, Nature methods, vol.12, issue.8, p.733, 2015.

H. Lopez-maestre, L. Brinza, C. Marchet, J. Kielbassa, S. Bastien et al., Snp calling from rna-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence, Nucleic acids research, vol.44, issue.19, pp.148-148, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01352586

M. Madoui, S. Engelen, C. Cruaud, C. Belser, L. Bertrand et al., Genome assembly using nanopore-guided long and error-free dna reads, BMC genomics, vol.16, issue.1, p.327, 2015.
DOI : 10.1186/s12864-015-1519-z

URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1519-z

F. Mahé, T. Rognes, C. Quince, C. De-vargas, and M. Dunthorn, Swarm: robust and fast clustering method for amplicon-based studies, PeerJ, vol.2, p.593, 2014.

N. Maillet, G. Collet, T. Vannier, D. Lavenier, P. et al., COMMET: comparing and combining multiple metagenomic datasets, Bioinformatics and Biomedicine (BIBM), pp.94-98, 2014.
DOI : 10.1109/bibm.2014.6999135

URL : https://hal.archives-ouvertes.fr/hal-01080050

N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. et al., Compareads: comparing huge metagenomic experiments, BMC bioinformatics, vol.13, p.10, 2012.
DOI : 10.1186/1471-2105-13-s19-s10

URL : https://hal.archives-ouvertes.fr/hal-00760332

U. Manber and G. Myers, Suffix arrays: a new method for on-line string searches, siam Journal on Computing, vol.22, issue.5, pp.935-948, 1993.
DOI : 10.1137/0222058

URL : http://webglimpse.net/pubs/suffix.pdf

C. Marchet, L. Lecompte, C. Da-silva, C. Cruaud, J. M. Aury et al., Clustering de novo by gene of long reads from transcriptomics data. bioRxiv, p.170035, 2018.
DOI : 10.1101/170035

URL : https://hal.archives-ouvertes.fr/hal-01643156

C. Marchet, L. Lecompte, A. Limasset, L. Bittner, P. et al., A resource-frugal probabilistic dictionary and applications in bioinformatics, Discrete Applied Mathematics, 2018.
DOI : 10.1016/j.dam.2018.03.035

URL : https://hal.archives-ouvertes.fr/hal-01873312

C. Marchet, A. Limasset, L. Bittner, P. , and P. , A resource-frugal probabilistic dictionary and applications in (meta)genomics, Proceedings of the Prague Stringology Conference, pp.85-97, 2016.
DOI : 10.1016/j.dam.2018.03.035

URL : https://hal.archives-ouvertes.fr/hal-01386744

G. Marsaglia, Xorshift rngs, Journal of Statistical Software, vol.8, issue.14, pp.1-6, 2003.
DOI : 10.18637/jss.v008.i14

URL : https://www.jstatsoft.org/index.php/jss/article/view/v008i14/xorshift.pdf

J. A. Martin and Z. Wang, Next-generation transcriptome assembly, Nature Reviews Genetics, vol.12, issue.10, p.671, 2011.
DOI : 10.1038/nrg3068

URL : https://digital.library.unt.edu/ark:/67531/metadc830328/m2/1/high_res_d/1076789.pdf

A. G. Matera and Z. Wang, A day in the life of the spliceosome, Nature reviews Molecular cell biology, vol.15, issue.2, p.108, 2014.

E. M. Mccreight, A space-economical suffix tree construction algorithm, Journal of the ACM (JACM), vol.23, issue.2, pp.262-272, 1976.

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.

J. Mei, J. Zhao, X. Yang, and W. Zhou, Remote protein homology detection using a modularity-based approach, Information Science and Technology (ICIST), pp.1287-1291, 2011.
DOI : 10.1109/icist.2011.5765074

A. Meng, C. Marchet, E. Corre, P. Peterlongo, A. Alberti et al., A de novo approach to disentangle partner identity and function in holobiont systems, 2017.
DOI : 10.1186/s40168-018-0481-9

URL : https://hal.archives-ouvertes.fr/hal-01643153

A. Meng, C. Marchet, E. Corre, P. Peterlongo, A. Alberti et al., A de novo approach to disentangle partner identity and function in holobiont systems, 2017.
DOI : 10.1186/s40168-018-0481-9

URL : https://hal.archives-ouvertes.fr/hal-01643153

G. Miclotte, M. Heydari, P. Demeester, S. Rombauts, Y. Van-de-peer et al., Jabba: hybrid error correction for long sequencing reads, Algorithms for Molecular Biology, vol.11, issue.1, p.10, 2016.
DOI : 10.1186/s13015-016-0075-7

URL : https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0075-7

V. Miele, S. Penel, V. Daubin, F. Picard, D. Kahn et al., High-quality sequence clustering guided by network topology and multiple alignment likelihood, Bioinformatics, vol.28, issue.8, pp.1078-1085, 2012.
DOI : 10.1093/bioinformatics/bts098

URL : https://hal.archives-ouvertes.fr/hal-00965711

B. Modrek and C. Lee, A genomic view of alternative splicing, Nature genetics, vol.30, issue.1, pp.13-19, 2002.
DOI : 10.1038/ng0102-13

R. D. Morin, M. Bainbridge, A. Fejes, M. Hirst, M. Krzywinski et al., Profiling the hela s3 transcriptome using randomly primed cdna and massively parallel short-read sequencing, Biotechniques, vol.45, issue.1, p.81, 2008.
DOI : 10.2144/000112900

URL : https://www.future-science.com/doi/pdf/10.2144/000112900

R. Mott, Est genome: a program to align spliced dna sequences to unspliced genomic dna, Bioinformatics, vol.13, issue.4, pp.477-478, 1997.

G. Muller-parker, C. F. Cook, and C. B. , Interactions between corals and their symbiotic algae, Coral Reefs in the Anthropocene, pp.99-116, 2015.

G. Myers, Efficient local alignment discovery amongst noisy long reads, International Workshop on Algorithms in Bioinformatics, pp.52-67, 2014.

G. Myers, Efficient local alignment discovery amongst noisy long reads, International Workshop on Algorithms in Bioinformatics, pp.52-67, 2014.

S. B. Needleman and C. D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of molecular biology, vol.48, issue.3, pp.443-453, 1970.

M. E. Newman, The structure and function of complex networks, SIAM review, vol.45, issue.2, pp.167-256, 2003.

M. E. Newman, Detecting community structure in networks, The European Physical Journal B, vol.38, issue.2, pp.321-330, 2004.

M. E. Newman, Fast algorithm for detecting community structure in networks, Physical review E, vol.69, issue.6, p.66133, 2004.

P. Novák, P. Neumann, and J. Macas, Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data, BMC bioinformatics, vol.11, issue.1, p.378, 2010.

S. Oikonomopoulos, Y. C. Wang, H. Djambazian, D. Badescu, R. et al., Benchmarking of the oxford nanopore minion sequencing for quantitative and qualitative assessment of cdna populations, Scientific reports, vol.6, p.31602, 2016.

B. D. Ondov, T. J. Treangen, P. Melsted, A. B. Mallonee, N. H. Bergman et al., Mash: fast genome and metagenome distance estimation using minhash, Genome biology, vol.17, issue.1, p.132, 2016.

Y. Ono, K. Asai, and M. Hamada, Pbsim: Pacbio reads simulator-toward accurate genome assembly, Bioinformatics, vol.29, issue.1, pp.119-121, 2013.

A. Oshlack, M. D. Robinson, Y. , and M. D. , From rna-seq reads to differential expression results, Genome biology, vol.11, issue.12, p.220, 2010.

G. Palla, A. Barabási, and T. Vicsek, Quantifying social group evolution, Nature, vol.446, issue.7136, pp.664-667, 2007.

Q. Pan, O. Shai, L. J. Lee, B. J. Frey, and B. J. Blencowe, Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, Nature genetics, vol.40, issue.12, p.1413, 2008.

J. A. Pardalos and M. Resende, On maximum cli, ue problems in very large graphs, 1999.

R. Patro, G. Duggal, K. , and C. , Salmon: accurate, versatile and ultrafast quantification from rna-seq data using lightweight-alignment. bioRxiv, p.21592, 2015.

R. Patro, S. M. Mount, K. , and C. , Sailfish enables alignment-free isoform quantification from rna-seq reads using lightweight algorithms, Nature biotechnology, vol.32, issue.5, p.462, 2014.

J. Pattillo, A. Veremyev, S. Butenko, and V. Boginski, On the maximum quasi-clique problem, Discrete Applied Mathematics, vol.161, issue.1-2, pp.244-257, 2013.

J. E. Pérez-ortín, P. Alepuz, S. Chávez, and M. Choder, Eukaryotic mrna decay: methodologies, pathways, and links to other stages of gene expression, Journal of molecular biology, vol.425, issue.20, pp.3750-3775, 2013.

G. Pertea, X. Huang, F. Liang, V. Antonescu, R. Sultana et al., Tigr gene indices clustering tools (tgicl): a software system for fast clustering of large est datasets, Bioinformatics, vol.19, issue.5, pp.651-652, 2003.

S. Pesant, F. Not, M. Picheral, S. Kandels-lewis, N. Le-bescot et al., Open science resources for the discovery and analysis of tara oceans data, vol.2, p.150023, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01253984

N. Philippe, M. Salson, T. Commes, and E. Rivals, Crac: an integrated approach to the analysis of rna-seq reads, Genome Biology, vol.14, issue.3, p.30, 2013.
URL : https://hal.archives-ouvertes.fr/inserm-00850972

J. H. Pinzón, B. Kamel, C. A. Burge, C. D. Harvell, M. Medina et al., Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral, Royal Society open science, vol.2, issue.4, p.140214, 2015.

O. Porrua and D. Libri, Rna quality control in the nucleus: the angels' share of rna, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, vol.1829, issue.6, pp.604-611, 2013.

E. M. Poursani, B. M. Soltani, and S. J. Mowla, Differential expression of oct4 pseudogenes in pluripotent and tumor cell lines, Cell Journal (Yakhteh), vol.18, issue.1, p.28, 2016.

I. Probert, R. Siano, C. Poirier, J. Decelle, T. Biard et al., Brandtodinium gen. nov. and b. nutricula comb. nov.(dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians, Journal of phycology, vol.50, issue.2, pp.388-399, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01140979

J. Quackenbush, F. Liang, I. Holt, G. Pertea, U. et al., The tigr gene indices: reconstruction and representation of expressed gene sequences, Nucleic Acids Research, vol.28, issue.1, pp.141-145, 2000.

F. Radicchi, C. Castellano, F. Cecconi, V. Loreto, and D. Parisi, Defining and identifying communities in networks, Proceedings of the National Academy of Sciences of the United States of America, vol.101, issue.9, pp.2658-2663, 2004.

U. N. Raghavan, R. Albert, and S. Kumara, Near linear time algorithm to detect community structures in large-scale networks, Physical review E, vol.76, issue.3, p.36106, 2007.

J. Reuter, D. V. Spacek, and M. Snyder, High-throughput sequencing technologies, Molecular Cell, vol.58, issue.4, pp.586-597, 2015.

A. Reyes, S. Anders, and W. Huber, Analyzing RNA-seq data for differential exon usage with the DEXSeq package, 2012.

G. Rizk, D. Lavenier, C. , and R. , Dsk: k-mer counting with very low memory usage, Bioinformatics, vol.29, issue.5, pp.652-653, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00778473

G. Rizk, D. Lavenier, C. , and R. , DSK: K-mer counting with very low memory usage, Bioinformatics, vol.29, issue.5, pp.652-653, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00778473

M. Roberts, W. Hayes, B. R. Hunt, S. M. Mount, and J. A. Yorke, Reducing storage requirements for biological sequence comparison, Bioinformatics, vol.20, issue.18, pp.3363-3369, 2004.

G. Robertson, J. Schein, R. Chiu, R. Corbett, M. Field et al., De novo assembly and analysis of RNA-seq data, Nature methods, vol.7, issue.11, pp.909-912, 2010.

J. T. Robinson, H. Thorvaldsdóttir, W. Winckler, M. Guttman, E. S. Lander et al., Integrative genomics viewer, Nature biotechnology, vol.29, issue.1, p.24, 2011.

G. E. Rodwell, R. Sonu, J. M. Zahn, J. Lund, J. Wilhelmy et al., A transcriptional profile of aging in the human kidney, PLoS biology, vol.2, issue.12, p.427, 2004.

F. Rohwer, V. Seguritan, F. Azam, and N. Knowlton, Diversity and distribution of coralassociated bacteria, Marine Ecology Progress Series, vol.243, pp.1-10, 2002.

I. G. Romero, A. A. Pai, J. Tung, G. , and Y. , Rna-seq: impact of rna degradation on transcript quantification, BMC biology, vol.12, issue.1, p.42, 2014.

G. Sacomoto, B. Sinaimeri, C. Marchet, V. Miele, M. Sagot et al., Navigating in a sea of repeats in rna-seq without drowning, International Workshop on Algorithms in Bioinformatics, pp.82-96, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01079947

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, vol.13, issue.6, p.5, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00784407

M. K. Sakharkar, V. T. Chow, K. , and P. , Distributions of exons and introns in the human genome, In silico biology, vol.4, issue.4, pp.387-393, 2004.

L. Salmela and E. Rivals, Lordec: accurate and efficient long read error correction. Bioinformatics, vol.30, pp.3506-3514, 2014.
URL : https://hal.archives-ouvertes.fr/lirmm-01100451

L. Salmela and J. Schröder, Correcting errors in short reads by multiple alignments, Bioinformatics, vol.27, issue.11, pp.1455-1461, 2011.

L. Salmela, R. Walve, E. Rivals, and E. Ukkonen, Accurate self-correction of errors in long reads using de bruijn graphs, Bioinformatics, vol.33, issue.6, pp.799-806, 2016.
URL : https://hal.archives-ouvertes.fr/lirmm-01385006

F. Sanger, S. Nicklen, and A. R. Coulson, Dna sequencing with chain-terminating inhibitors, Proceedings of the national academy of sciences, vol.74, pp.5463-5467, 1977.

N. Sangwan, F. Xia, G. , and J. A. , Recovering complete and draft population genomes from metagenome datasets, vol.4, p.8, 2016.

D. Sankoff, Simultaneous solution of the rna folding, alignment and protosequence problems, SIAM journal on applied mathematics, vol.45, issue.5, pp.810-825, 1985.

E. E. Schadt, S. A. Monks, T. A. Drake, and A. J. Lusis, Genetics of gene expression surveyed in maize, mouse and man, Nature, vol.422, issue.6929, p.297, 2003.

G. D. Schuler, Pieces of the puzzle: expressed sequence tags and the catalog of human genes, Journal of Molecular Medicine, vol.75, issue.10, pp.694-698, 1997.

M. H. Schulz, D. R. Zerbino, M. Vingron, and E. Birney, Oases: robust de novo rna-seq assembly across the dynamic range of expression levels, Bioinformatics, vol.28, issue.8, pp.1086-1092, 2012.

J. A. Schwarz, P. B. Brokstein, C. Voolstra, A. Y. Terry, D. J. Miller et al., Coral life history and symbiosis: functional genomic resources for two reef building caribbean corals, acropora palmata and montastraea faveolata, BMC genomics, vol.9, issue.1, p.97, 2008.

M. Selosse and C. Strullu-derrien, Origins of the terrestrial flora: a symbiosis with fungi, BIO Web of Conferences, vol.4, p.9, 2015.

J. K. Senior, Partitions and their representative graphs, American Journal of Mathematics, vol.73, issue.3, pp.663-689, 1951.

D. Sharon, H. Tilgner, F. Grubert, and M. Snyder, A single-molecule long-read survey of the human transcriptome, Nature biotechnology, vol.31, issue.11, pp.1009-1014, 2013.

S. Shen, J. W. Park, J. Huang, K. A. Dittmar, Z. Lu et al., MATS: a bayesian framework for flexible detection of differential alternative splicing from RNA-seq data, Nucleic acids research, p.1291, 2012.

A. Siegl, J. Kamke, T. Hochmuth, J. Piel, M. Richter et al., Single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges, The ISME journal, vol.5, issue.1, p.61, 2011.

R. L. Simister, P. Deines, E. S. Botté, N. S. Webster, T. et al., Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms, Environmental Microbiology, vol.14, issue.2, pp.517-524, 2012.

J. T. Simpson, R. E. Workman, P. Zuzarte, M. David, L. Dursi et al., Detecting dna cytosine methylation using nanopore sequencing, nature methods, vol.14, issue.4, p.407, 2017.

T. F. Smith and M. S. Waterman, Comparison of biosequences, Advances in applied mathematics, vol.2, pp.482-489, 1981.

R. Smith-unna, C. Boursnell, R. Patro, J. M. Hibberd, K. et al., Transrate: referencefree quality assessment of de novo transcriptome assemblies, Genome research, vol.26, issue.8, pp.1134-1144, 2016.

C. Soderlund, E. Johnson, M. Bomhoff, and A. Descour, Pave: program for assembling and viewing ests, Bmc Genomics, vol.10, issue.1, p.1, 2009.

L. Song and L. Florea, Rcorrector: efficient and accurate error correction for illumina rna-seq reads, Gigascience, vol.4, issue.1, p.48, 2015.

L. Song, L. Florea, L. , and B. , Lighter: fast and memory-efficient sequencing error correction without counting, Genome biology, vol.15, issue.11, p.509, 2014.

I. Sovi´csovi´c, M. Siki´csiki´c, A. Wilm, S. N. Fenlon, S. Chen et al., Fast and sensitive mapping of nanopore sequencing reads with graphmap, Nature communications, p.7, 2016.

B. K. Stöcker, J. Köster, R. , and S. , Simlord: Simulation of long read data, vol.32, pp.2704-2706, 2016.

S. Sunagawa, L. P. Coelho, S. Chaffron, J. R. Kultima, K. Labadie et al., Structure and function of the global ocean microbiome, Science, vol.348, issue.6237, p.1261359, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01233742

J. Tazi, N. Bakkour, and S. Stamm, Alternative splicing and disease, Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, vol.1792, issue.1, pp.14-26, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00562867

N. M. Thanh, H. Jung, R. E. Lyons, I. Njaci, B. Yoon et al., Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (pangasianodon hypophthalmus), Marine genomics, vol.23, pp.87-97, 2015.

J. D. Thompson, D. G. Higgins, and T. J. Gibson, Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic acids research, vol.22, issue.22, pp.4673-4680, 1994.

H. Tilgner, F. Jahanbani, I. Gupta, P. Collier, E. Wei et al., Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome, Genome research, vol.28, issue.2, pp.231-242, 2018.

G. Tischler and E. W. Myers, Non hybrid long read consensus using local de bruijn graph assembly. bioRxiv, p.106252, 2017.

D. C. Torney, C. Burks, D. Davison, and K. M. Sirotkin, Computation of d2: a measure of sequence dissimilarity, Computers and DNA: the proceedings of the Interface between Computation Science and Nucleic Acid Sequencing Workshop, 1988.

A. Toseland, S. Moxon, T. Mock, and V. Moulton, Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation, BMC genomics, vol.15, issue.1, p.901, 2014.

C. Trapnell, L. Pachter, and S. L. Salzberg, Tophat: discovering splice junctions with rna-seq, Bioinformatics, vol.25, issue.9, pp.1105-1111, 2009.

C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature protocols, vol.7, issue.3, pp.562-578, 2012.

M. L. Tress, B. Bodenmiller, R. Aebersold, and A. Valencia, Proteomics studies confirm the presence of alternative protein isoforms on a large scale, Genome biology, vol.9, issue.11, p.162, 2008.

J. J. Turunen, E. H. Niemelä, B. Verma, and M. J. Frilander, The significant other: splicing by the minor spliceosome, Wiley Interdisciplinary Reviews: RNA, vol.4, issue.1, pp.61-76, 2013.

R. Vaser, I. Sovic, N. Nagarajan, and M. Sikic, Fast and accurate de novo genome assembly from long uncorrected reads. bioRxiv, p.68122, 2016.

R. Vaser, I. Sovi´csovi´c, N. Nagarajan, and M. , Fast and accurate de novo genome assembly from long uncorrected reads, Genome research, vol.27, issue.5, pp.737-746, 2017.

B. Wang, E. Tseng, M. Regulski, T. A. Clark, T. Hon et al., Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing, Nature communications, vol.7, p.11708, 2016.

G. Wang and T. A. Cooper, Splicing in disease: disruption of the splicing code and the decoding machinery, Nature Reviews Genetics, vol.8, issue.10, p.2164, 2007.

K. Wang, D. Singh, Z. Zeng, S. J. Coleman, Y. Huang et al., Mapsplice: accurate mapping of rna-seq reads for splice junction discovery, Nucleic acids research, vol.38, issue.18, pp.178-178, 2010.

Y. Wang, H. C. Leung, S. Yiu, C. , and F. Y. , Metacluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample, Bioinformatics, vol.28, issue.18, pp.356-362, 2012.

Z. Wang, M. Gerstein, and M. Snyder, Rna-seq: a revolutionary tool for transcriptomics, Nature reviews genetics, vol.10, issue.1, p.57, 2009.

D. J. Watts and S. H. Strogatz, Collective dynamics of 'small-world'networks, nature, vol.393, issue.6684, p.440, 1998.

N. S. Webster and M. W. Taylor, Marine sponges and their microbial symbionts: love and other relationships, Environmental Microbiology, vol.14, issue.2, pp.335-346, 2012.

Z. Wei, S. Zhang, and Y. Zhang, Dmclust, a density-based modularity method for accurate otu picking of 16s rrna sequences, Molecular informatics, issue.12, p.36, 2017.

J. L. Weirather, M. De-cesare, Y. Wang, P. Piazza, V. Sebastiano et al., Comprehensive comparison of pacific biosciences and oxford nanopore technologies and their applications to transcriptome analysis, 1000.

D. E. Wood and S. L. Salzberg, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome biology, vol.15, issue.3, p.46, 2014.

T. D. Wu, J. Reeder, M. Lawrence, G. Becker, and M. J. Brauer, Gmap and gsnap for genomic sequence alignment: enhancements to speed, accuracy, and functionality, Statistical Genomics: Methods and Protocols, pp.283-334, 2016.

T. D. Wu and C. K. Watanabe, Gmap: a genomic mapping and alignment program for mrna and est sequences, Bioinformatics, vol.21, issue.9, pp.1859-1875, 2005.

C. Xiao, Y. Chen, S. Xie, K. Chen, Y. Wang et al., Mecat: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads, nature methods, vol.14, issue.11, p.1072, 2017.

Y. Xie, G. Wu, J. Tang, R. Luo, J. Patterson et al., Soapdenovo-trans: de novo transcriptome assembly with short rna-seq reads, Bioinformatics, vol.30, issue.12, pp.1660-1666, 2014.

C. Yang, J. Chu, R. L. Warren, and I. Birol, Nanosim: nanopore sequence read simulator based on statistical characterization, GigaScience, vol.6, issue.4, pp.1-6, 2017.

J. Yang and J. Leskovec, Defining and evaluating network communities based on ground-truth, Knowledge and Information Systems, vol.42, issue.1, pp.181-213, 2015.

X. Yang, S. P. Chockalingam, A. , and S. , A survey of error-correction methods for nextgeneration sequencing, Briefings in bioinformatics, vol.14, issue.1, pp.56-66, 2012.

Y. Yang and S. A. Smith, Optimizing de novo assembly of short-read rna-seq data for phylogenomics, BMC genomics, vol.14, issue.1, p.328, 2013.

C. Ye and Z. S. Ma, Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads, PeerJ, vol.4, p.2016, 2016.

M. Zhao, W. Lee, E. P. Garrison, M. , and G. T. , Ssw library: an simd smith-waterman c/c++ library for use in genomic applications, PloS one, vol.8, issue.12, p.82138, 2013.

E. Zorita, P. Cuscó, and G. J. Filion, Starcode: sequence clustering based on all-pairs search, Bioinformatics, vol.31, issue.12, pp.1913-1919, 2015.

E. Zorita, P. Cusco, and G. J. Filion, Starcode: sequence clustering based on all-pairs search, Bioinformatics, vol.31, issue.12, pp.1913-1919, 2015.

M. Zuker and D. Sankoff, Rna secondary structures and their prediction, Bulletin of mathematical biology, vol.46, issue.4, pp.591-621, 1984.