A comprehensive study of de novo genome assemblers: current challenges and future prospective, Evol Bioinforma Online, vol.14, 2018. ,
Piercing the dark matter: bioinformatics of long-range sequencing and mapping, Nat Rev Genet, vol.19, p.329, 2018. ,
New approaches for genome assembly and scaffolding, Annu Rev AnimBiosci, vol.7, pp.17-40, 2019. ,
Genome structural variation discovery and genotyping, Nat Rev Genet, vol.12, pp.363-76, 2011. ,
GAGE: a critical evaluation of genome assemblies and assembly algorithms, Genome Res, vol.22, pp.557-67, 2012. ,
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, vol.2, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00868822
A comparative evaluation of genome assembly reconciliation tools, Genome Biol, vol.18, p.93, 2017. ,
Comprehensive mapping of longrange interactions reveals folding principles of the human genome, Science, vol.326, pp.289-93, 2009. ,
Capturing chromosome conformation, Science, vol.295, pp.1306-1317, 2002. ,
Contact genomics: scaffolding and phasing (meta) genomes using chromosome 3D physical signatures, FEBS Lett, vol.589, pp.2966-74, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01419996
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions, Nat Biotechnol, vol.31, pp.1119-1144, 2013. ,
High-throughput genome scaffolding from in vivo DNA interaction frequency, Nat Biotechnol, vol.31, pp.1143-1150, 2013. ,
High-quality genome (re) assembly using chromosomal contact data, Nat Commun, vol.5, p.5695, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01138788
A probabilistic approach for genome assembly from high-throughput chromosome conformation capture data ,
, Université Pierre et Marie Curie -Paris 6, 2013.
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms, eLife, vol.3, p.3318, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01316684
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome, Nat Genet, vol.49, pp.643-50, 2017. ,
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds, Science, vol.356, pp.92-97, 2017. ,
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage, Genome Res, vol.26, pp.342-50, 2016. ,
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay, Sci Adv, vol.3, p.1602105, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02866658
Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes, BiotechnolBiofuels, vol.10, p.151, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01581813
Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus, New Phytol, vol.214, pp.219-251, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01402123
The Ectocarpus genome and the independent evolution of multicellularity in brown algae, Nature, vol.465, pp.617-638, 2010. ,
URL : https://hal.archives-ouvertes.fr/cea-00906990
OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus, Proc Natl Acad Sci, vol.108, pp.11518-11541, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01806390
A haploid system of sex determination in the brown alga Ectocarpus sp, Curr Biol, vol.24, pp.1945-57, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01132642
Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae, vol.8, p.43101, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02042404
High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga, Ectocarpus. Sci Rep, vol.7, p.43241, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01510346
Making contacts on a nucleic acid polymer, Trends Biochem Sci, vol.26, pp.733-773, 2001. ,
UntersuchungenzurEntwicklungsgeschichte der BraunalgeEctocarpussiliculosusAusNeapel, Planta, vol.68, pp.57-68, 1966. ,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015. ,
Versatile genome assembly evaluation with QUAST-LG, Bioinformatics, vol.34, pp.142-50, 2018. ,
The MaSuRCA genome assembler, Bioinformatics, vol.29, pp.2669-77, 2013. ,
Life history and taxonomy of two populations of ligulate Desmarestia (Phaeophyceae) from Chile, Can J Bot, vol.64, pp.2948-54, 1986. ,
Integrating Hi-C links with assembly graphs for chromosome-scale assembly, PLoS Comput Biol, vol.15, p.1007273, 2019. ,
Normalization of a chromosomal contact map, BMC Genomics, vol.13, p.436, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00769663
Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Nat Methods, vol.9, pp.999-1003, 2012. ,
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nat Genet, vol.43, pp.1059-65, 2011. ,
Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C, Mol Syst Biol, vol.14, p.8293, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01890095
Shifting the limits in wheat research and breeding using a fully annotated reference genome, Consortium (IWGSC) TIWGS, Investigators IR principal, vol.361, p.7191, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01885399
CAMSA: a tool for comparative analysis and merging of scaffold assemblies, BMC Bioinformatics, vol.18, p.496, 2017. ,
Metassembler: merging and optimizing de novo genome assemblies, Genome Biol, vol.16, p.207, 2015. ,
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology, PLoS One, vol.7, p.47768, 2012. ,
Fast and accurate de novo genome assembly from long uncorrected reads, Genome Res, vol.27, pp.737-783, 2017. ,
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement, PLoS One, vol.9, p.112963, 2014. ,
HyPo: super fast accurate polisher for long read genome assemblies. bioRxiv, 2019. ,
hybridSPAdes: an algorithm for hybrid assembly of short and long reads, Bioinformatics, vol.32, pp.1009-1024, 2016. ,
Hybrid assembly with long and short reads improves discovery of gene family expansions, BMC Genomics, vol.18, p.541, 2017. ,
Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle, EMBO J, vol.36, issue.18, pp.2684-97, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01596511
Large genome reassembly based on Hi-C data, continuation of GRAAL. Sequence Read Archive. Datasets, 2020. ,
Large genome reassembly based on Hi-C data, continuation of GRAAL, 2019. ,
Large genome reassembly based on Hi-C data, continuation of GRAAL, 2019. ,
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