10.5.2 Multiple contig borders between t and next(t) Correct node id for next(t), p.89 ,
Approximate string matching using a bidirectional index, Theor. Comput. Sci, pp.145-158, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-00824706
Using cascading Bloom filters to improve the memory usage for de Brujin graphs, BMC Algorithms for Molecular Biology, vol.9191, issue.70, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00824697
Improved compression of DNA sequencing data with Cascading Bloom filters In: Special issue of the, IJFCS) for the international Student Conference on Mathematical Foundations in Bioinformatics (MatBio), 2017. ,
Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid, In: Nature, vol.1714356, issue.12, pp.737-738, 1953. ,
Big Data: Astronomical or Genomical?, PLOS Biology, vol.28, issue.7, pp.1-11, 2015. ,
DOI : 10.1371/journal.pbio.1002195.s006
URL : https://doi.org/10.1371/journal.pbio.1002195
Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science, vol.304, issue.5667, pp.66-74, 2004. ,
DOI : 10.1126/science.1093857
A Holistic Approach to Marine Eco-Systems Biology, PLoS Biology, vol.6, issue.10, 2011. ,
DOI : 10.1371/journal.pbio.1001177.g002
URL : https://hal.archives-ouvertes.fr/hal-00691580
A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.13, issue.7285, pp.59-65, 2010. ,
DOI : 10.1101/gr.229202. Article published online before March 2002
URL : https://hal.archives-ouvertes.fr/cea-00908974
TerraGenome: a consortium for the sequencing of a soil metagenome, Nature Reviews Microbiology, vol.5, issue.4, pp.252-252, 2009. ,
DOI : 10.1038/nrmicro2119
URL : https://hal.archives-ouvertes.fr/hal-00391653
The NIH Human Microbiome Project, Genome Research, vol.1912, pp.2317-2323, 2009. ,
High Throughput Short Read Alignment via Bi-directional BWT, 2009 IEEE International Conference on Bioinformatics and Biomedicine, pp.31-36, 2009. ,
DOI : 10.1109/BIBM.2009.42
Molecular Configuration in Sodium Thymonucleate, Nature, vol.1714356, pp.740-741, 1953. ,
A new method for sequencing DNA., Proceedings of the National Academy of Sciences, vol.74, issue.2, pp.560-564, 1977. ,
DOI : 10.1073/pnas.74.2.560
DNA sequencing with chain-terminating inhibitors, Proceedings of the National Academy of Sciences of the United States of America, 1977. ,
DOI : 10.1073/pnas.74.12.5463
URL : http://www.pnas.org/content/74/12/5463.full.pdf
Next-Generation DNA Sequencing Methods, Annual Review of Genomics and Human Genetics, vol.9, issue.1, pp.387-402, 2008. ,
DOI : 10.1146/annurev.genom.9.081307.164359
A decade???s perspective on DNA sequencing technology, Nature, vol.364, issue.7333, 2011. ,
DOI : 10.1056/NEJMoa1012928
Sequencing technologies ??? the next generation, Nature Reviews Genetics, vol.37, issue.1, pp.31-46, 2010. ,
DOI : 10.1016/j.tig.2007.12.006
The properties and applications of single-molecule DNA sequencing, Genome Biology, vol.122, 2011. ,
Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, issue.7057, p.14, 2005. ,
DOI : 10.1089/cmb.1995.2.275
Performance comparison of whole-genome sequencing platforms, Nature Biotechnology, vol.30, issue.1, pp.78-82, 2011. ,
DOI : 10.1038/nbt.1975
Historical Perspective, Development and Applications of Next-Generation Sequencing in Plant Virology, Viruses, vol.66, issue.1, 2014. ,
DOI : 10.3390/v3101849
A review of DNA sequencing techniques, Quarterly Reviews of Biophysics, vol.35, issue.02, pp.169-200, 2002. ,
DOI : 10.1017/S0033583502003797
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences, S4, pp.14-76, 2011. ,
Next-Generation Sequencing ??? An Overview of the History, Tools, and ???Omic??? Applications, p.61964 ,
DOI : 10.5772/61964
The Diploid Genome Sequence of an Individual Human, PLoS Biology, vol.17, issue.10, 2007. ,
DOI : 10.1371/journal.pbio.0050254.sd001
The complete genome of an individual by massively parallel DNA sequencing, Nature, vol.2, issue.7189, 2008. ,
DOI : 10.1101/gr.8.3.175
Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data, PLoS Computational Biology, vol.6, issue.4, 2013. ,
DOI : 10.1371/journal.pcbi.1003031.s014
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing, BMC Genomics, vol.23, issue.21, 2011. ,
DOI : 10.1093/bioinformatics/btm404
Accuracy and quality of massively parallel DNA pyrosequencing, Genome Biology, vol.87, 2007. ,
A Practical Minimal Perfect Hashing Method, pp.488-500, 2005. ,
DOI : 10.1007/11427186_42
Monotone Minimal Perfect Hashing: Searching a Sorted Table with <italic>O</italic>(1) Accesses, Proceedings of the Twentieth Annual ACM-SIAM Symposium on Discrete Algorithms, pp.785-794, 2009. ,
Fast and scalable minimal perfect hashing for massive key sets, p.16 ,
URL : https://hal.archives-ouvertes.fr/hal-01566246
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
Less hashing, same performance: Building a better Bloom filter " . In: Random Struct, Algorithms, vol.33, issue.2, pp.187-218, 2008. ,
DOI : 10.1002/rsa.20208
URL : http://www.eecs.harvard.edu/~michaelm/postscripts/rsa2008.pdf
Linear Pattern Matching Algorithms SWAT '73, Proceedings of the 14th Annual Symposium on Switching and Automata Theory, 1973. ,
DOI : 10.1109/swat.1973.13
URL : http://airelles.i3s.unice.fr/files/Weiner.pdf
A Space-Economical Suffix Tree Construction Algorithm, Journal of the ACM, vol.23, issue.2, pp.262-272, 1976. ,
DOI : 10.1145/321941.321946
On-line construction of suffix trees, Algorithmica, vol.10, issue.3, pp.249-260, 1995. ,
DOI : 10.1145/321941.321946
Optimal suffix tree construction with large alphabets, Proceedings 38th Annual Symposium on Foundations of Computer Science, pp.137-143, 1997. ,
DOI : 10.1109/SFCS.1997.646102
OASIS, Proceedings of the 29th international conference on Very large data bases, pp.910-921, 2003. ,
DOI : 10.1016/B978-012722442-8/50085-9
Alignment of whole genomes, Nucleic Acids Research, vol.7, issue.4, pp.2369-2376, 1999. ,
DOI : 10.1101/gr.7.4.315
Suffix Arrays: A New Method for On-Line String Searches, Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms. SODA '90, pp.319-327, 1990. ,
DOI : 10.1137/0222058
Information Retrieval, Chap. New Indices for Text: PAT Trees and PAT Arrays, pp.66-82, 1992. ,
Simple Linear Work Suffix Array Construction The Netherlands, Languages and Programming: 30th International Colloquium, ICALP 2003 Eindhoven, pp.943-9553, 2003. ,
Linear Suffix Array Construction by Almost Pure Induced-Sorting, 2009 Data Compression Conference, pp.193-202, 2009. ,
DOI : 10.1109/DCC.2009.42
A taxonomy of suffix array construction algorithms, ACM Computing Surveys, vol.39, issue.2, 2007. ,
DOI : 10.1145/1242471.1242472
Replacing suffix trees with enhanced suffix arrays, Journal of Discrete Algorithms, vol.2, issue.1, pp.53-86, 2004. ,
DOI : 10.1016/S1570-8667(03)00065-0
URL : https://doi.org/10.1016/s1570-8667(03)00065-0
Fast sequence clustering using a suffix array algorithm, Bioinformatics, vol.19, issue.10, 2003. ,
DOI : 10.1093/bioinformatics/btg138
Replacing suffix trees with enhanced suffix arrays, Journal of Discrete Algorithms, vol.2, issue.1, pp.53-86, 2004. ,
DOI : 10.1016/S1570-8667(03)00065-0
URL : https://doi.org/10.1016/s1570-8667(03)00065-0
Fast and sensitive mapping of bisulfitetreated sequencing data, Bioinformatics, vol.2813, issue.19, pp.1698-1704, 2012. ,
A block-sorting lossless data compression algorithm, 1994. ,
Opportunistic data structures with applications, Proceedings 41st Annual Symposium on Foundations of Computer Science, pp.390-398, 2000. ,
DOI : 10.1109/SFCS.2000.892127
A block-sorting lossless data compression algorithm, California, vol.19, p.31, 1994. ,
High-order Entropy-compressed Text Indexes, Proceedings of the Fourteenth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA '03, pp.841-850, 2003. ,
DOI : 10.1007/978-3-642-40273-9_14
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, pp.25-31, 2009. ,
DOI : 10.1186/gb-2009-10-3-r25
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.9, issue.11, pp.1754-1760, 2009. ,
DOI : 10.1186/1471-2105-9-128
URL : https://academic.oup.com/bioinformatics/article-pdf/25/14/1754/605544/btp324.pdf
Efficient de novo assembly of large genomes using compressed data structures, Genome Research, vol.22, issue.3, pp.549-556, 2012. ,
DOI : 10.1101/gr.126953.111
Approximate String Matching with Compressed Indexes, Algorithms, vol.1, issue.3, pp.1105-1136, 2009. ,
DOI : 10.1145/135239.135244
URL : https://doi.org/10.3390/a2031105
Bidirectional search in a string with wavelet trees and bidirectional matching statistics, Information and Computation, vol.213, pp.13-22, 2012. ,
DOI : 10.1016/j.ic.2011.03.007
Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform, Proc. 21st European Symposium on Algorithms (ESA). 2013, pp.133-144 ,
DOI : 10.1007/978-3-642-40450-4_12
Novel computational techniques for mapping and classifying Next- Generation Sequencing data, p.94 ,
A survey of sequence alignment algorithms for next-generation sequencing, Briefings in Bioinformatics, vol.10, issue.9, pp.473-483, 2010. ,
DOI : 10.1186/gb-2009-10-9-r98
Short-Read Mapping Bioinformatics for High Throughput Sequencing, pp.107-125 ,
Short Read Mapping: An Algorithmic Tour, Proceedings of the IEEE, vol.105, issue.3, pp.1-23, 2015. ,
DOI : 10.1109/JPROC.2015.2455551
URL : http://europepmc.org/articles/pmc5425171?pdf=render
A fast string searching algorithm, Communications of the ACM, vol.20, issue.10, pp.762-772, 1977. ,
DOI : 10.1145/359842.359859
Fast Pattern Matching in Strings, SIAM Journal on Computing, vol.6, issue.2, 1977. ,
DOI : 10.1137/0206024
String-matching and other products, Symposium on Complexity of Computation: SIAM-AMS Proceedings, pp.113-125, 1974. ,
Improved string matching with k mismatches, ACM SIGACT News, vol.17, issue.4, pp.52-54, 1986. ,
DOI : 10.1145/8307.8309
Faster algorithms for string matching with k mismatches, Journal of Algorithms, vol.50, issue.2, pp.257-275, 2004. ,
DOI : 10.1016/S0196-6774(03)00097-X
Fast string matching with k differences, Journal of Computer and System Sciences, vol.37, issue.1, pp.63-78, 1988. ,
DOI : 10.1016/0022-0000(88)90045-1
URL : https://doi.org/10.1016/0022-0000(88)90045-1
An improved algorithm for approximate string matching, Automata, Languages and Programming: 16th International Colloquium Stresa, Italy, pp.394-404, 1989. ,
Amino acid substitution matrices from protein blocks., Proceedings of the National Academy of Sciences, vol.89, issue.22, pp.10915-10919, 1992. ,
DOI : 10.1073/pnas.89.22.10915
URL : http://www.pnas.org/content/89/22/10915.full.pdf
A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.483, pp.443-453, 1970. ,
Identification of common molecular subsequences(81 ) 90087 -5. url: http : / / www . sciencedirect . com / science, Journal of molecular biology, vol.1471, pp.195-202, 1981. ,
A fast bit-vector algorithm for approximate string matching based on dynamic programming, Journal of the ACM, vol.463, pp.395-415, 1999. ,
Improved tools for biological sequence comparison., Proceedings of the National Academy of Sciences, vol.85, issue.8, p.55, 1988. ,
DOI : 10.1073/pnas.85.8.2444
SOAP: short oligonucleotide alignment program, Bioinformatics, vol.5, issue.5, pp.713-714, 2008. ,
DOI : 10.1038/nrg1325
URL : https://academic.oup.com/bioinformatics/article-pdf/24/5/713/527122/btn025.pdf
SOAP2: an improved ultrafast tool for short read alignment, Bioinformatics, vol.456, issue.7218, pp.1966-1967, 2009. ,
DOI : 10.1038/nature07484
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping, PLoS ONE, vol.8, issue.3, 2014. ,
DOI : 10.1371/journal.pone.0090581.s008
BFAST: an alignment tool for large scale genome resequencing In: PloS one 4, 2009. ,
Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Research, vol.18, issue.11, pp.1851-1858, 2008. ,
DOI : 10.1101/gr.078212.108
URL : http://genome.cshlp.org/content/18/11/1851.full.pdf
Updates to the RMAP short-read mapping software, Bioinformatics, vol.5251, issue.11, pp.2841-2842, 2009. ,
DOI : 10.1007/978-3-540-87361-7_4
ZOOM! Zillions of oligos mapped, Bioinformatics, vol.124, issue.1, p.29, 2008. ,
DOI : 10.1016/j.cell.2005.10.043
SHRiMP2: Sensitive yet Practical Short Read Mapping, Bioinformatics, vol.26, issue.7, 2011. ,
DOI : 10.1093/bioinformatics/btq057
URL : https://academic.oup.com/bioinformatics/article-pdf/27/7/1011/16902170/btr046.pdf
YASS: enhancing the sensitivity of DNA similarity search In: Nucleic acids research 33, Web Server issue, 2005. ,
PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002. ,
DOI : 10.1093/bioinformatics/18.3.440
URL : https://academic.oup.com/bioinformatics/article-pdf/18/3/440/648219/180440.pdf
Better Filtering with Gapped q-Grams, Combinatorial Pattern Matching: 12th Annual Symposium, pp.73-85, 2001. ,
DOI : 10.1007/3-540-48194-X_6
URL : http://www.mpi-sb.mpg.de/~juha/publications/fundamenta-revised.ps.gz
SeqMap: mapping massive amount of oligonucleotides to the genome, Bioinformatics, vol.14, issue.8, pp.2395-2396, 2008. ,
DOI : 10.1261/rna.1070208
A, Journal of Bioinformatics and Computational Biology, vol.04, p.2, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00824706
Compressed full-text indexes, ACM Computing Surveys, vol.39, issue.1, p.31, 2007. ,
DOI : 10.1145/1216370.1216372
URL : http://www.dcc.uchile.cl/TR/2006/TR_DCC-2006-006.pdf
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, p.75, 2009. ,
DOI : 10.1186/gb-2009-10-3-r25
poster Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013 (cit, p.31 ,
Compressed indexing and local alignment of DNA, Bioinformatics, vol.14, issue.6, pp.791-797, 2008. ,
DOI : 10.1109/69.979973
Fast and accurate long-read alignment with Burrows???Wheeler transform, Bioinformatics, vol.7, issue.5, pp.589-595, 2010. ,
DOI : 10.1089/10665270050081478
URL : https://academic.oup.com/bioinformatics/article-pdf/26/5/589/16896917/btp698.pdf
Fast and accurate short read alignment with Burrows- Wheeler transform " . en, In: Bioinformatics, vol.2514, pp.31-75, 2009. ,
DOI : 10.1093/bioinformatics/btp324
URL : https://academic.oup.com/bioinformatics/article-pdf/25/14/1754/605544/btp324.pdf
Poisson Approximation for Dependent Trials, The Annals of Probability, vol.3, issue.3, pp.534-545, 1975. ,
DOI : 10.1214/aop/1176996359
URL : http://doi.org/10.1214/aop/1176996359
Poisson approximation, 1992. ,
Fast Approximate Search in Large Dictionaries, Computational Linguistics, vol.22, issue.1, pp.451-477, 2004. ,
DOI : 10.1002/spe.4380250307
Faster Filters for Approximate String Matching, Proc. 9th Workshop on Algorithm Engineering and Experiments (ALENEX), pp.84-90, 2007. ,
DOI : 10.1137/1.9781611972870.8
Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph, Briefings in Functional Genomics, vol.24, issue.24, 2012. ,
DOI : 10.1093/bioinformatics/btn548
A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies, PLoS ONE, vol.215, issue.3, 2011. ,
DOI : 10.1371/journal.pone.0017915.s003
GAGE: A critical evaluation of genome assemblies and assembly algorithms, Genome Research, vol.22, issue.3, pp.557-567, 2011. ,
DOI : 10.1101/gr.131383.111
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, GigaScience, vol.215, issue.3, pp.2047-217, 2013. ,
DOI : 10.1016/S0022-2836(05)80360-2
URL : https://hal.archives-ouvertes.fr/hal-00868822
Assembly algorithms for next-generation sequencing data, Genomics, vol.95, issue.6, pp.315-327, 2010. ,
DOI : 10.1016/j.ygeno.2010.03.001
A mew computer method for the storage and manipulation of DNA gel reading data, Nucleic Acids Research, vol.8, issue.16, 1980. ,
DOI : 10.1093/nar/8.16.3673
ARACHNE: A Whole-Genome Shotgun Assembler, Genome Research, vol.12, issue.1, pp.177-189, 2002. ,
DOI : 10.1101/gr.208902
A Whole-Genome Assembly of Drosophila, Science, vol.287, issue.5461, pp.5461-2196, 2000. ,
DOI : 10.1126/science.287.5461.2196
CAP3: A DNA Sequence Assembly Program, Genome Research, vol.9, issue.9, pp.868-877, 1999. ,
DOI : 10.1101/gr.9.9.868
PCAP: A Whole-Genome Assembly Program, Genome Research, vol.13, issue.9, pp.2164-2170, 2003. ,
DOI : 10.1101/gr.1390403
Assembling Genomic DNA Sequences with PHRAP, 2007. ,
DOI : 10.1016/0022-2836(81)90087-5
The Phusion Assembler, Genome Research, vol.13, issue.1, pp.81-90, 2003. ,
DOI : 10.1101/gr.731003
Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, issue.7057, 2005. ,
DOI : 10.1089/cmb.1995.2.275
Efficient de novo assembly of large genomes using compressed data structures, Genome Research, vol.22, issue.3, pp.549-556, 2012. ,
DOI : 10.1101/gr.126953.111
Approximate all-pairs suffix/prefix overlaps, Information and Computation, vol.213, pp.49-58, 2012. ,
DOI : 10.1016/j.ic.2012.02.002
Faster Filters for Approximate String Matching, Proceedings of the Ninth Workshop on Algorithm Engineering and Experiments (ALENEX), pp.84-90, 2007. ,
DOI : 10.1137/1.9781611972870.8
Improved Filters for the Approximate Suffix-Prefix Overlap Problem, String Processing and Information Retrieval: 21st International Symposium, SPIRE 2014, Ouro Preto, Brazil, pp.139-148978, 2014. ,
DOI : 10.1007/978-3-319-11918-2_14
URL : https://hal.archives-ouvertes.fr/hal-01086208
An Eulerian path approach to DNA fragment assembly, Proc. Natl. Acad. Sci. U.S.A. 98, pp.9748-9753, 2001. ,
DOI : 10.1126/science.1058040
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-652, 2011. ,
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
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
Meta-IDBA: a de Novo assembler for metagenomic data, Bioinformatics, vol.4, issue.12, pp.94-101, 2011. ,
DOI : 10.1371/journal.pone.0008407
Succinct data structures for assembling large genomes, Bioinformatics, vol.18, issue.Suppl. 1, pp.479-486, 2011. ,
DOI : 10.1101/gr.074492.107
Exploiting sparseness in de novo genome assembly, S1. url, p.55, 2012. ,
DOI : 10.1093/bioinformatics/btr319
Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter, Algorithms in Bioinformatics -12th International Workshop, WABI 2012, pp.236-248, 2012. ,
DOI : 10.1007/978-3-642-33122-0_19
URL : https://hal.archives-ouvertes.fr/hal-00868805
Succinct de Bruijn Graphs, Algorithms in Bioinformatics -12th International Workshop, WABI 2012, pp.225-235, 2012. ,
DOI : 10.1007/978-3-642-33122-0_18
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs, Proceedings of the National Academy of Sciences, vol.54, issue.2, pp.13272-13277, 2012. ,
DOI : 10.1090/S0002-9947-1943-0012401-3
GATB: Genome Assembly & Analysis Tool Box, Bioinformatics, vol.18, issue.20, pp.2959-2961, 2014. ,
DOI : 10.1101/gr.074492.107
URL : https://hal.archives-ouvertes.fr/hal-01088571
Variable-Order de Bruijn Graphs, 2015 Data Compression Conference, pp.383-392, 2015. ,
DOI : 10.1109/DCC.2015.70
URL : http://arxiv.org/pdf/1411.2718.pdf
Bidirectional Variable-Order de Bruijn Graphs, LATIN 2016: Theoretical Informatics -12th Latin American Symposium, pp.164-178978, 2016. ,
DOI : 10.1007/978-3-662-49529-2_13
On the Representation of De Bruijn Graphs, Proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology, pp.35-55978, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01524525
Fully Dynamic de Bruijn Graphs, String Processing and Information Retrieval -23rd International Symposium, SPIRE 2016, pp.145-152978, 2016. ,
DOI : 10.1101/gr.074492.107
URL : http://arxiv.org/pdf/1607.04909
DSK: k-mer counting with very low memory usage, Bioinformatics, vol.12, issue.6, pp.652-655, 2013. ,
DOI : 10.1186/1471-2105-12-333
URL : https://hal.archives-ouvertes.fr/hal-00778473
The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.1453-1462, 1997. ,
DOI : 10.1126/science.277.5331.1453
An Optimal Bloom Filter Replacement Based on Matrix Solving, Proceedings. Lecture Notes in Computer Science, vol.32, issue.1, pp.263-273, 2009. ,
DOI : 10.1109/TIT.1986.1057137
Fast lossless compression via cascading Bloom filters, BMC Bioinformatics, vol.15, issue.Suppl 9, pp.70-72, 2014. ,
DOI : 10.1038/nmeth.1923
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-15-S9-S7?site=bmcbioinformatics.biomedcentral.com
Compression of FASTQ and SAM Format Sequencing Data, PLoS ONE, vol.32, issue.3, 2013. ,
DOI : 10.1371/journal.pone.0059190.s001
Efficient storage of high throughput DNA sequencing data using reference-based compression, Genome Research, vol.215, pp.734-740, 2011. ,
Compression of next-generation sequencing reads aided by highly efficient de novo assembly, Nucleic Acids Research, vol.26, issue.7, 2012. ,
DOI : 10.1186/1471-2105-12-354
Reference-based compression of short-read sequences using path encoding, Bioinformatics, vol.31, issue.12, 2015. ,
DOI : 10.1007/978-3-319-05269-4_31
Compressing Genomic Sequence Fragments Using SlimGene Lecture Notes in Computer Science, Computational Molecular Biology. Ed. by B. Berger, vol.6044, issue.20, pp.310-324978, 2010. ,
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph, BMC Bioinformatics, vol.43, issue.2, pp.12859-12874, 2015. ,
DOI : 10.1093/nar/gku1187
URL : https://hal.archives-ouvertes.fr/hal-01214682
Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform, Bioinformatics, vol.6, issue.17, 2012. ,
DOI : 10.1186/1748-7188-6-23
Compression of DNA sequence reads in FASTQ format, Bioinformatics, vol.26, issue.6, 2011. ,
DOI : 10.1093/bioinformatics/btq346
Disk-based compression of data from genome sequencing, Bioinformatics, vol.6, issue.9, 2014. ,
DOI : 10.1186/1748-7188-6-23
SCALCE: boosting sequence compression algorithms using locally consistent encoding, Bioinformatics, vol.24, issue.23, 2012. ,
DOI : 10.1109/TIT.1978.1055934
URL : https://academic.oup.com/bioinformatics/article-pdf/28/23/3051/18530674/bts593.pdf
BEETL-fastq: a searchable compressed archive for DNA reads, Bioinformatics, vol.32, issue.5, 2014. ,
DOI : 10.1038/nbt.2835
Data-dependent bucketing improves reference-free compression of sequencing reads, Bioinformatics, vol.31, issue.17, 2015. ,
DOI : 10.1038/nbt.3170
Integrative analysis of environmental sequences using MEGAN4, Genome Research, vol.21, issue.9, p.75, 2011. ,
DOI : 10.1101/gr.120618.111
Metagenomic microbial community profiling using unique cladespecific marker genes, pp.811-814, 2012. ,
DOI : 10.1038/nmeth.2066
URL : http://europepmc.org/articles/pmc3443552?pdf=render
MetaPhyler: Taxonomic profiling for metagenomic sequences, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) ,
DOI : 10.1109/BIBM.2010.5706544
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs, Proceedings of the National Academy of Sciences, vol.54, issue.2, 2012. ,
DOI : 10.1090/S0002-9947-1943-0012401-3
URL : http://www.pnas.org/content/109/33/13272.full.pdf
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides, BMC Research Notes, vol.5, issue.1, 2012. ,
DOI : 10.1371/journal.pone.0003373
Scalable metagenomic taxonomy classification using a reference genome database, Bioinformatics, vol.304, issue.18, 2013. ,
DOI : 10.1126/science.1093857
RefSeq microbial genomes database: new representation and annotation strategy, Nucleic Acids Research, vol.42, pp.1-553, 2014. ,
DOI : 10.1093/nar/gkv278
URL : https://academic.oup.com/nar/article-pdf/43/7/3872/7211719/gkv278.pdf
Kraken: ultrafast metagenomic sequence classification using exact alignments R46. doi: 10.1186/ gb-2014-15-3-r46. url: http://www.pubmedcentral.nih.gov/articlerender, In: Genome biology, vol.153, p.94, 2014. ,
DOI : 10.1186/gb-2014-15-3-r46
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2014-15-3-r46?site=genomebiology.biomedcentral.com
Centrifuge: rapid and sensitive classification of metagenomic sequences In: bioRxiv preprints, 2016. ,
Fast gapped-read alignment with Bowtie 2, Nature methods 9, pp.357-366, 2012. ,
DOI : 10.1093/bioinformatics/btp352
Fast and sensitive taxonomic classification for metagenomics with Kaiju, Nature Communications, vol.7, 2016. ,
Classification of DNA sequences using Bloom filters, Bioinformatics, vol.7, issue.13, 2010. ,
DOI : 10.1089/10665270050081478
CoMeta: Classification of Metagenomes Using kmers, PLOS ONE, vol.10, issue.4, 2015. ,
An evaluation of the accuracy and speed of metagenome analysis tools, In: Scientific Reports, vol.6, 2016. ,
Evaluating techniques for metagenome annotation using simulated sequence data, FEMS Microbiology Ecology, vol.15, issue.7, 2016. ,
DOI : 10.1093/bioinformatics/btr595
Evaluating performance of metagenomic characterization algorithms using in silico datasets generated with FASTQSim, 2016. ,
DOI : 10.1101/046532
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities, BMC Bioinformatics, vol.4, issue.3, p.363, 2015. ,
DOI : 10.6026/97320630004046
Comparing K-mer based methods for improved classification of 16S sequences, BMC Bioinformatics, vol.6, issue.1, 2015. ,
DOI : 10.1038/ismej.2011.82
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies: http://www.la-press. com/metagenomics-tools-and-insights-for-analyzing-next-generation- sequenci-article-a4809, Bioinformatics and Biology Insights, 2015. ,
Compact Pat Trees, 1996. ,