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
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
Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology, vol.34, issue.5, pp.525-527, 2016. ,
DOI : 10.1093/bioinformatics/bts480
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
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
Computational pan-genomics: status, promises and challenges, Briefings in Bioinformatics, p.89, 2016. ,
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
Using referencefree compressed data structures to analyse sequencing reads from thousands of human genomes, p.60186, 2016. ,
PanCake: A data structure for pangenomes, German Conference on Bioinformatics, pp.35-45, 2013. ,
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
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
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
Open source clustering software, Bioinformatics, vol.20, issue.9, pp.1453-1454, 2004. ,
DOI : 10.1093/bioinformatics/bth078
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
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
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
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303, p.3997, 2013. ,
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
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
Genome-Scale Algorithm Design, 2015. ,
DOI : 10.1017/CBO9781139940023
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
A resource-frugal probabilistic dictionary and applications in (meta) genomics. arXiv preprint, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01322440
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
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
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
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity, p.75481, 2016. ,
Adding compression to block addressing inverted indexes, Information Retrieval, vol.3, issue.1, pp.49-77, 2000. ,
DOI : 10.1023/A:1009934302807
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
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
-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
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
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
Fast search of thousands of short-read sequencing experiments, Nature Biotechnology, vol.34, issue.3, pp.300-302, 2016. ,
DOI : 10.1093/bioinformatics/btr011
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
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
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
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
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