U. Baier, T. Beller, and E. Ohlebusch, Graphical pan-genome analysis with compressed suffix trees and the Burrows???Wheeler transform, Bioinformatics, vol.32, issue.4, p.603, 2015.
DOI : 10.1093/bioinformatics/btv603

B. H. Bloom, Space/time trade-offs in hash coding with allowable errors, Communications of the ACM, vol.13, issue.7, pp.422-426, 1970.
DOI : 10.1145/362686.362692

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.20.2080

N. L. Bray, H. Pimentel, P. Melsted, and L. Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology, vol.34, issue.5, pp.525-527, 2016.
DOI : 10.1093/bioinformatics/bts480

S. Chambi, D. Lemire, O. Kaser, and R. Godin, Better bitmap performance with roaring bitmaps. Software: practice and experience, p.709719, 2015.
DOI : 10.1002/spe.2325

URL : http://arxiv.org/pdf/1402.6407

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.1, 2013.
DOI : 10.1007/978-3-642-33122-0_19

URL : https://hal.archives-ouvertes.fr/hal-00753930

C. P. Consortium, Computational pan-genomics: status, promises and challenges, Briefings in Bioinformatics, p.89, 2016.

A. Crainiceanu and D. Lemire, Bloofi: Multidimensional Bloom filters, Information Systems, vol.54, pp.311-324, 2015.
DOI : 10.1016/j.is.2015.01.002

URL : http://arxiv.org/abs/1501.01941

D. D. Dolle, Z. Liu, M. L. Cotten, J. T. Simpson, Z. Iqbal et al., Using referencefree compressed data structures to analyse sequencing reads from thousands of human genomes, p.60186, 2016.

C. Ernst and S. Rahmann, PanCake: A data structure for pangenomes, German Conference on Bioinformatics, pp.35-45, 2013.

S. Gog, T. Beller, A. Moffat, and M. Petri, From Theory to Practice: Plug and Play with Succinct Data Structures, International Symposium on Experimental Algorithms, pp.326-337, 2014.
DOI : 10.1007/978-3-319-07959-2_28

URL : http://arxiv.org/abs/1311.1249

Y. Heo, X. L. Wu, D. Chen, J. Ma, and W. M. Hwu, BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads, Bioinformatics, vol.30, issue.10, p.30, 2014.
DOI : 10.1093/bioinformatics/btu030

G. Holley, R. Wittler, and J. Stoye, Bloom Filter Trie ??? A Data Structure for Pan-Genome Storage, In: Algorithms in Bioinformatics, pp.217-230, 2015.
DOI : 10.1007/978-3-662-48221-6_16

M. J. De-hoon, S. Imoto, J. Nolan, and S. Miyano, Open source clustering software, Bioinformatics, vol.20, issue.9, pp.1453-1454, 2004.
DOI : 10.1093/bioinformatics/bth078

A. Kirsch and M. Mitzenmacher, Less hashing, same performance: Building a better Bloom filter, Random Structures and Algorithms, vol.32, issue.2, pp.187-218, 2008.
DOI : 10.1017/CBO9780511814075

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.152.579

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

R. Leinonen, H. Sugawara, and M. Shumway, The Sequence Read Archive, Nucleic Acids Research, vol.39, issue.Database, p.1019, 2010.
DOI : 10.1093/nar/gkq1019

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013647

H. Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303, p.3997, 2013.

B. Liu, D. Zhu, and Y. Wang, deBWT: parallel construction of Burrows???Wheeler Transform for large collection of genomes with de Bruijn-branch encoding, Bioinformatics, vol.32, issue.12, pp.174-182, 2016.
DOI : 10.1093/bioinformatics/btw266

P. R. Loh, M. Baym, and B. Berger, Compressive genomics, Nature Biotechnology, vol.37, issue.7, pp.627-630, 2012.
DOI : 10.1093/nar/gkn788

URL : http://www.nature.com/nbt/journal/v30/n7/pdf/nbt.2241.pdf

V. Mäkinen, D. Belazzougui, F. Cunial, and A. I. Tomescu, Genome-Scale Algorithm Design, 2015.
DOI : 10.1017/CBO9781139940023

G. Marçais and C. Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, vol.27, issue.6, pp.764-770, 2011.
DOI : 10.1093/bioinformatics/btr011

C. Marchet, A. Limasset, L. Bittner, and P. Peterlongo, A resource-frugal probabilistic dictionary and applications in (meta) genomics. arXiv preprint, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01322440

S. Marcus, H. Lee, and M. C. Schatz, SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips, Bioinformatics, vol.30, issue.24, pp.3476-3483, 2014.
DOI : 10.1093/bioinformatics/btu756

P. Melsted and J. K. Pritchard, Efficient counting of k-mers in DNA sequences using a bloom filter, BMC Bioinformatics, vol.12, issue.1, p.333, 2011.
DOI : 10.1038/nature09534

I. Minkin, S. Pham, and P. Medvedev, TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes, Bioinformatics, p.609, 2016.
DOI : 10.1093/bioinformatics/btw609

URL : http://arxiv.org/abs/1602.05856

K. D. Murray, C. Webers, C. S. Ong, J. O. Borevitz, and N. Warthmann, kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity, p.75481, 2016.

G. Navarro, E. S. De-moura, M. Neubert, N. Ziviani, and R. Baeza-yates, Adding compression to block addressing inverted indexes, Information Retrieval, vol.3, issue.1, pp.49-77, 2000.
DOI : 10.1023/A:1009934302807

A. Nellore, L. Collado-torres, A. E. Jaffe, J. Alquicira-hernndez, C. Wilks et al., Rail-RNA: scalable analysis of RNA-seq splicing and coverage, Bioinformatics p, p.575, 2016.
DOI : 10.1093/bioinformatics/btw575

URL : https://academic.oup.com/bioinformatics/article-pdf/doi/10.1093/bioinformatics/btw575/7704807/btw575.pdf

R. Patro, S. M. Mount, and C. Kingsford, Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms, Nature Biotechnology, vol.23, issue.5, pp.462-464, 2014.
DOI : 10.1093/bioinformatics/btp120

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077321

R. Raman, V. Raman, and S. S. Rao, -ary trees, prefix sums and multisets, Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms, pp.233-242, 2002.
DOI : 10.1145/1290672.1290680

URL : https://hal.archives-ouvertes.fr/halshs-01061298

R. Rozov, R. Shamir, and E. Halperin, Fast lossless compression via cascading Bloom filters, BMC Bioinformatics, vol.15, issue.Suppl 9, p.1, 2014.
DOI : 10.1038/nmeth.1923

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-15-S9-S7?site=bmcbioinformatics.biomedcentral.com

K. Salikhov, G. Sacomoto, and G. Kucherov, Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs, Bioinformatics Lecture Notes in Computer Science, vol.8126, pp.364-376, 2013.
DOI : 10.1007/978-3-642-40453-5_28

URL : https://hal.archives-ouvertes.fr/hal-00824697

B. Solomon and C. Kingsford, Fast search of thousands of short-read sequencing experiments, Nature Biotechnology, vol.34, issue.3, pp.300-302, 2016.
DOI : 10.1093/bioinformatics/btr011

H. Stranneheim, M. Käller, T. Allander, B. Andersson, L. Arvestad et al., Classification of DNA sequences using Bloom filters, Bioinformatics, vol.26, issue.13, pp.1595-1600, 2010.
DOI : 10.1093/bioinformatics/btq230

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887045

C. Sun, R. S. Harris, R. Chikhi, and P. Medvedev, Allsome sequence bloom trees, bioRxiv, vol.1202, p.90464, 2016.
DOI : 10.1007/978-3-319-56970-3_17

URL : https://hal.archives-ouvertes.fr/hal-01575350

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.
DOI : 10.1038/nbt0710-691

Y. W. Yu, N. M. Daniels, D. C. Danko, and B. Berger, Entropy-Scaling Search of Massive Biological Data, Cell Systems, vol.1, issue.2, pp.130-140, 2015.
DOI : 10.1016/j.cels.2015.08.004

URL : http://doi.org/10.1016/j.cels.2015.08.004

N. Ziviani, E. S. De-moura, G. Navarro, and R. Baeza-yates, Compression: a key for next-generation text retrieval systems, Computer, vol.33, issue.11, pp.37-44, 2000.
DOI : 10.1109/2.881693

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.21.2271