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

D. Jones, W. Ruzzo, X. Peng, and M. Katze, Compression of next-generation sequencing reads aided by highly efficient de novo assembly, Nucleic Acids Research, vol.40, issue.22, 2012.
DOI : 10.1093/nar/gks754

M. Fritz, R. Leinonen, G. Cochrane, and E. Birney, Efficient storage of high throughput sequencing data using reference-based compression

C. Kingsford and R. Patro, Reference-based compression of short-read sequences using path encoding, Bioinformatics, vol.31, issue.12, p.71, 2015.
DOI : 10.1093/bioinformatics/btv071

J. Bonfield and M. Mahoney, Compression of FASTQ and SAM Format Sequencing Data, PLoS ONE, vol.32, issue.3, 2013.
DOI : 10.1371/journal.pone.0059190.s001

F. Hach, I. Numanagic, C. Alkan, and S. Sahinalp, SCALCE: boosting sequence compression algorithms using locally consistent encoding, Bioinformatics, vol.28, issue.23, pp.3051-057, 2012.
DOI : 10.1093/bioinformatics/bts593

S. Deorowicz and S. Grabowski, Compression of DNA sequence reads in FASTQ format, Bioinformatics, vol.27, issue.6, pp.860-862, 2011.
DOI : 10.1093/bioinformatics/btr014

S. Grabowski, S. Deorowicz, and ?. Roguski, Disk-based compression of data from genome sequencing, Bioinformatics, vol.31, issue.9, p.844, 2014.
DOI : 10.1093/bioinformatics/btu844

L. Janin, O. Schulz-trieglaff, and A. Cox, BEETL-fastq: a searchable compressed archive for DNA reads, Bioinformatics, vol.30, issue.19, p.387, 2014.
DOI : 10.1093/bioinformatics/btu387

R. Patro and C. Kingsford, Data-dependent bucketing improves reference-free compression of sequencing reads, Bioinformatics, vol.31, issue.17, p.248, 2015.
DOI : 10.1093/bioinformatics/btv248

A. Cox, M. Bauer, T. Jakobi, and G. Rosone, Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform, Bioinformatics, vol.28, issue.11, pp.1415-1424, 2012.
DOI : 10.1093/bioinformatics/bts173

R. Wan, V. Anh, and K. Asai, Transformations for the compression of FASTQ quality scores of next-generation sequencing data, Bioinformatics, vol.28, issue.5, pp.628-663, 2012.
DOI : 10.1093/bioinformatics/btr689

R. Cánovas, A. Moffat, and A. Turpin, Lossy compression of quality scores in genomic data, Bioinformatics, vol.30, issue.15, pp.2130-136, 2014.
DOI : 10.1093/bioinformatics/btu183

L. Janin, G. Rosone, and A. Cox, Adaptive reference-free compression of sequence quality scores, Bioinformatics, vol.30, issue.1, p.257, 2013.
DOI : 10.1093/bioinformatics/btt257

Y. Yu, D. Yorukoglu, and B. Berger, Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification, Research in computational molecular biology, pp.385-99, 2014.
DOI : 10.1007/978-3-319-05269-4_31

A. Kirsch and M. Mitzenmacher, Less hashing, same performance: Building a better bloom filter. Algorithms-ESA, pp.2006456-67, 2006.

R. Chikhi and P. Medvedev, Informed and automated k-mer size selection for genome assembly, Bioinformatics, vol.30, issue.1, p.310, 2013.
DOI : 10.1093/bioinformatics/btt310
URL : https://hal.archives-ouvertes.fr/hal-01477511

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.226-258, 2012.
DOI : 10.1016/0198-8859(91)90078-N

J. Pell, A. Hintze, R. Canino-koning, A. Howe, J. Tiedje et al., Scaling metagenome sequence assembly with probabilistic de Bruijn graphs, Proceedings of the National Academy of Sciences, vol.109, issue.33, pp.13272-13279, 2012.
DOI : 10.1073/pnas.1121464109

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, pp.22-32, 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, Algoritm Bioinforma, vol.9, pp.364-76, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00824697

I. Witten, R. Neal, and J. Cleary, Arithmetic coding for data compression, Communications of the ACM, vol.30, issue.6, pp.520-540, 1987.
DOI : 10.1145/214762.214771

E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre et al., GATB: Genome Assembly & Analysis Tool Box, Bioinformatics, vol.30, issue.20
DOI : 10.1093/bioinformatics/btu406
URL : https://hal.archives-ouvertes.fr/hal-01088571

G. Rizk, D. Lavenier, and R. Chikhi, DSK: k-mer counting with very low memory usage, Bioinformatics, vol.29, issue.5, pp.652-655, 2013.
DOI : 10.1093/bioinformatics/btt020
URL : https://hal.archives-ouvertes.fr/hal-00778473

S. Deorowicz, M. Kokot, S. Grabowski, and A. Debudaj-grabysz, KMC 2: fast and resource-frugal k-mer counting, Bioinformatics, vol.31, issue.10, p.22, 2015.
DOI : 10.1093/bioinformatics/btv022

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.2078-079, 2009.
DOI : 10.1093/bioinformatics/btp352

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009.
DOI : 10.1093/bioinformatics/btp324

Y. Yu, D. Yorukoglu, J. Peng, and B. Berger, Quality score compression improves genotyping accuracy, Nature Biotechnology, vol.33, issue.3, pp.240-243, 2015.
DOI : 10.1038/nmeth.1923

C. Lemaitre, L. Ciortuz, and P. Peterlongo, Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads, Algoritm Comput Biol, vol.8542, pp.119-149, 2014.
DOI : 10.1007/978-3-319-07953-0_10
URL : https://hal.archives-ouvertes.fr/hal-01063157

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