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Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees

 Camille Marchet , Antoine Limasset
2022
Pré-publication, Document de travail hal-03871213v1
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ELECTOR: EvaLuation of Error Correction Tools for lOng Reads

 Lolita Lecompte , Camille Marchet , Pierre Morisse , Antoine Limasset , Pierre Peterlongo , et al.
JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-2
Poster de conférence hal-01929900v1
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BLIGHT

 Camille Marchet , Antoine Limasset , Maël Kerbiriou
2017, ⟨swh:1:dir:e5e5dfd7345c521e1c211a16ae14115996bb9b5f;origin=https://hal.archives-ouvertes.fr/hal-04489902;visit=swh:1:snp:320be2f68227ca53ed1aa7f637b1f79288e7b732;anchor=swh:1:rel:96d6fee08fa540b75008627d049844c320b17fc8;path=/⟩
Logiciel hal-04489902v1
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Nouvelles approches pour l'exploitation des données de séquences génomique haut débit

 Antoine Limasset
Bio-informatique [q-bio.QM]. Université de Rennes, 2017. Français. ⟨NNT : 2017REN1S049⟩
Thèse tel-01686367v1

On the Representation of De Bruijn Graphs

 Rayan Chikhi , Antoine Limasset , Shaun Jackman , Jared T. Simpson , Paul Medvedev
Journal of Computational Biology, 2015, 22 (5), pp.336 - 352. ⟨10.1089/cmb.2014.0160⟩
Article dans une revue hal-01524525v1
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CONSENT

 Pierre Morisse , Camille Marchet , Antoine Limasset , Thierry Lecroq , Arnaud Lefebvre
2018, ⟨swh:1:dir:435ce7c73cfd3e0a70e78e70b324124b3a7b507b;origin=https://hal.archives-ouvertes.fr/hal-04442770;visit=swh:1:snp:8052f6a704123e9d53a08f2c142ebd6e9a29a800;anchor=swh:1:rel:29f2436e25a2800c24d0d26fdc90faa7cf0fe793;path=/⟩
Logiciel hal-04442770v1
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Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees

 Camille Marchet , Antoine Limasset
Recomb 2022- 26th Annual International Conference on Research in Computational Molecular Biology, May 2022, La jolla, United States
Communication dans un congrès hal-03832918v1

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

 Antoine Limasset , Jean-François Flot , Pierre Peterlongo
RECOMB 2018, Apr 2018, Paris, France
Communication dans un congrès hal-01644163v1

Locality-preserving minimal perfect hashing of k -mers

 Giulio Ermanno Pibiri , Yoshihiro Shibuya , Antoine Limasset
Bioinformatics, 2023, 39 (Supplement_1), pp.i534-i543. ⟨10.1093/bioinformatics/btad219⟩
Article dans une revue hal-04288471v1
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Fast and scalable minimal perfect hashing for massive key sets

 Antoine Limasset , Guillaume Rizk , Rayan Chikhi , Pierre Peterlongo
16th International Symposium on Experimental Algorithms, Jun 2017, London, United Kingdom. pp.1 - 11
Communication dans un congrès hal-01566246v1

Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors

 Coralie Rohmer , Hélène Touzet , Antoine Limasset
2023
Pré-publication, Document de travail hal-04288487v1
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Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

 Paul Simion , Jitendra Narayan , Antoine Houtain , Alessandro Derzelle , Lyam Baudry , et al.
Science Advances , 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩
Article dans une revue hal-03406292v1
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Read mapping on de Bruijn graphs

 Antoine Limasset , Bastien Cazaux , Eric Rivals , Pierre Peterlongo
BMC Bioinformatics, 2016, 17 (1), ⟨10.1186/s12859-016-1103-9⟩
Article dans une revue hal-01349636v1
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Locality-Preserving Minimal Perfect Hashing of k-mers

 Giulio Ermanno Pibiri , Yoshihiro Shibuya , Antoine Limasset
2022
Pré-publication, Document de travail hal-03832901v1
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A resource-frugal probabilistic dictionary and applications in (meta)genomics

 Camille Marchet , Antoine Limasset , Lucie Bittner , Pierre Peterlongo
Prageu Stringology Conference , Aug 2016, Prague, Czech Republic
Communication dans un congrès hal-01386744v1
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A resource-frugal probabilistic dictionary and applications in bioinformatics

 Camille Marchet , Lolita Lecompte , Antoine Limasset , Lucie Bittner , Pierre Peterlongo
Discrete Applied Mathematics, 2020, 92-102 (Volume 274), ⟨10.1016/j.dam.2018.03.035⟩
Article dans une revue hal-01322440v1
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Critical Assessment of Metagenome Interpretation: the second round of challenges

 Fernando Meyer , Adrian Fritz , Zhi-Luo Deng , David Koslicki , Till Robin Lesker , et al.
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Article dans une revue hal-03832903v1
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Efficient exact associative structure for sequencing data

 Camille Marchet , Maël Kerbiriou , Antoine Limasset
Recomb-Seq 2019 - 9th RECOMB Satellite Workshop on Massively Parallel Sequencing, May 2019, Whashinton, United States. pp.1-16
Communication dans un congrès hal-02435086v2
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Scalable long read self-correction and assembly polishing with multiple sequence alignment

 Pierre Morisse , Camille Marchet , Antoine Limasset , Thierry Lecroq , Arnaud Lefebvre
Scientific Reports, 2021, 11 (1), pp.1-13. ⟨10.1038/s41598-020-80757-5⟩
Article dans une revue hal-03210290v1
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ELECTOR : evaluator for long reads correction methods

 Camille Marchet , Pierre Morisse , Lolita Lecompte , Arnaud Lefebvre , Thierry Lecroq , et al.
NAR Genomics and Bioinformatics, 2020, 2 (1), pp.1-12. ⟨10.1093/nargab/lqz015⟩
Article dans une revue hal-02371117v1

NIQKI

 Clément Agret , Bastien Cazaux , Antoine Limasset
2022, ⟨swh:1:dir:4b130954e11adff2be9108f45c4181f972604407;origin=https://github.com/Malfoy/NIQKI;visit=swh:1:snp:65940e352a73e160a22b0e80a69d0b3964de4048;anchor=swh:1:rev:ac03f90a644e79c1a76a7e8d2dd0410470959a33⟩
Logiciel lirmm-04121986v1
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Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching

 Timothé Rouzé , Igor Martayan , Camille Marchet , Antoine Limasset
23rd International Workshop on Algorithms in Bioinformatics (WABI 2023, Sep 2023, Houston, United States. ⟨10.4230/LIPIcs.WABI.2023.15⟩
Communication dans un congrès hal-04279798v1
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supersampler Fractionnal hitting set implementation for lightweight genomic data sketching

 Antoine Limasset , Timothé Rouzé , Igor Martayan , Camille Marchet
2023, ⟨swh:1:dir:bb6dea99f95337e2bf26180f5242fa4b09b897f6;origin=https://hal.archives-ouvertes.fr/hal-04448163;visit=swh:1:snp:1f35ba3a6890c0ed7ca0e06e4662f5abc05db16c;anchor=swh:1:rel:42686bbd8658ab7a2a280c4dd46d8bd8223a0851;path=/⟩
Logiciel hal-04448163v1
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Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

 Antoine Limasset , Jean-François Flot , Pierre Peterlongo
Bioinformatics, 2019, ⟨10.1093/bioinformatics/btz102⟩
Article dans une revue hal-02407243v1
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lphash

 Antoine Limasset , Yoshihiro Shibuya , Giulio Ermanno Pibiri
2024, ⟨swh:1:dir:891ec55feff3e21e72d1f8cc20c8ac06d3eedf61;origin=https://hal.archives-ouvertes.fr/hal-04448111;visit=swh:1:snp:ea894566eed31b0f93dfed739d8e5dad5706be63;anchor=swh:1:rel:8fdbe9ff5721a3774892f2e56c211adf0fad7a95;path=/⟩
Logiciel hal-04448111v1
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Read correction for non-uniform coverages

 Camille Marchet , Yoann Dufresne , Antoine Limasset
2021
Pré-publication, Document de travail pasteur-03263392v1

BGREAT: A De Bruijn graph read mapping tool

 Antoine Limasset , Pierre Peterlongo
JOBIM 2015, Jul 2015, Clermont ferrant, France
Poster de conférence hal-01192857v1

BLight: efficient exact associative structure for k-mers

 Antoine Limasset , Camille Marchet , Mael Kerbiriou
Bioinformatics, 2021, 37 (18), pp.2858-2865. ⟨10.1093/bioinformatics/btab217⟩
Article dans une revue hal-03443183v1
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STRONG: metagenomics strain resolution on assembly graphs

 Antoine Limasset , Christopher Quince , Sergey Nurk , Sebastien Raguideau , Robert James , et al.
Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩
Article dans une revue hal-03443171v1
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Minimal perfect hash functions in large scale bioinformatics Problem

 Antoine Limasset , Camille Marchet , Pierre Peterlongo , Lucie Bittner
JOBIM 2016, Jun 2016, Lyon, France
Poster de conférence hal-01341718v1
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