Jean Mainguy

Publications

Article dans une revue (2)

Nested PCR to optimize rpoB metabarcoding for lowconcentration and host-associated bacterial DNA Laëtitia Leclerc,Gabryelle Agoutin,Thierry Brévault,Antony Champion,Jean Mainguyet al. Microbiology Spectrum, 2025, 13 (9), pp.e01417-25. ⟨10.1128/spectrum.01417-25⟩ Article dans une revue hal-05220858v1
Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes. Jean Mainguy,Claire Hoede Journal of Open Source Software, 2024, 9 (102), pp.6782. ⟨10.21105/joss.06782⟩ Article dans une revue hal-04722766v1

Communication dans un congrès (5)

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes Jérôme Arnoux,Jean Mainguy,Laura Bry,Quentin Fernandez De Grado,David Vallenetet al. The local pangenome, Oct 2023, Alicante, Spain Communication dans un congrès hal-04371302v1
PPanGGOLiN V2: technical enhancement and new features to analyze thousands of prokaryotic genomes Jean Mainguy,Jérôme Arnoux,Guillaume Gautreau,Adelme Bazin,David Vallenetet al. The local pangenome, Oct 2023, Alicante, Spain Communication dans un congrès hal-04371316v1
metagWGS : a workflow to analyse short or long HiFi metagenomic reads Joanna Fourquet,Maïna Vienne,Jean Mainguy,Vincent Darbot,Pierre Martinet al. Bioinfo Biosta Genotoul day, Dec 2022, Castanet-Tolosan, France Communication dans un congrès hal-03944382v1
The benefits of long read HiFi sequencing for metagenomic analysis Adrien Castinel,Jean Mainguy,Sylvie Combes,Carole Iampietro,Christine Gaspinet al. France génomique - VIIème Animation Wetlab et Bioinfo, Nov 2022, Strasbourg, France Communication dans un congrès hal-03896074v1
The benefits of long read HiFi sequencing for metabarcoding analysis Adrien Castinel,Jean Mainguy,Sylvie Combes,Carole Iampietro,Christine Gaspinet al. PACBIO DISCOVERIES ROADSHOW PARIS, PACBIO, May 2022, Paris, France Communication dans un congrès hal-03740586v1

Poster de conférence (12)

PanGBank: a database of pangenome graphs for comparative microbial genomics Jean Mainguy,Téo Lemane,Claudine Médigue,Alexandra Calteau,David Vallenet EAGS 2026 - International Environmental and Agronomical Genomics symposium, Feb 2026, Paris, France. Poster de conférence hal-05523557v1
Avancées réalisées en métabarcoding et en métagénomique dans le cadre du projet SeqOccIn grâce au séquençage longs fragments Denis Milan,Jean Mainguy,Adrien Castinel,Olivier Bouchez,Sylvie Combeset al. Colloque INRAE Genomics 2022, May 2022, Orléans, France. , 2022 Poster de conférence hal-03776011v1
metagWGS: a workflow to analyse short and long HiFi metagenomic reads Joanna Fourquet,Maïna Vienne,Jean Mainguy,Vincent Darbot,Pierre Martinet al. ECCB2022, Sep 2022, Sitges, Spain Poster de conférence hal-03788263v1
Implementation of new methods for metagenomics analysis using PacBio HiFi sequencing Adrien Castinel,Jean Mainguy,Sylvie Combes,Carole Iampietro,Christine Gaspinet al. Plant & Animal Genome Conference (PAG) 2022, Jan 2022, San Diego, United States Poster de conférence hal-03541346v1
metagWGS: a workflow to analyse short and long HiFi metagenomic reads Taxonomic profile HiFi vs Short reads assembly Joanna Fourquet,Jean Mainguy,Maïna Vienne,Céline Noirot,Pierre Martinet al. JOBIM 2022, Jul 2022, Rennes, France. Actes des exposés (keynotes, contributions orales, mini-symposia) : JOBIM2022_proceedings_oral.pdf (23 Mo) et actes des posters et démos : JOBIM2022_proceedings_posters_demos.pdf (19 Mo). ⟨10.15454/1.5572369328961167E12⟩ Poster de conférence hal-03771202v1
Strengths and limits of long read metabarcoding Jean Mainguy,Adrien Castinel,Olivier Bouchez,Sylvie Combes,Carole Iampietroet al. ECCB 2022, Sep 2022, Meliá Sitges, Spain Poster de conférence hal-03848228v1
Benefits of PacBio HiFi long reads for metagenomic whole genome analysis Adrien Castinel,Jean Mainguy,Olivier Bouchez,Sylvie Combes,Carole Iampietroet al. Environmental And Agronomical Genomics Symposium, Oct 2021, Tours, France Poster de conférence hal-03538657v1
A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis Carole Iampietro,Camille Eché,Adrien Castinel,Rémy-Félix Serre,Christophe Kloppet al. PAG XXVIII, Plant and Animal Genome, Jan 2020, San Diego, United States. 2020 Poster de conférence hal-02947690v1
Improving microbial taxonomic profiling with long read technologies Jean Mainguy,Adrien Castinel,Olivier Bouchez,Sylvie Combes,Carole Iampietroet al. JOBIM2020, Jun 2020, Online, France Poster de conférence hal-03177058v1
Des solutions informatiques innovantes pour l’utilisation et le développement de biomarqueurs de diversité du microbiote. Maria Bernard,Olivier Rué,Malo Le Boulch,Jean Mainguy,Laurent Cauquilet al. DefisPHASE 2019, 2019, Rennes, France Poster de conférence hal-03851900v1
Identification of genomic regions for high-resolution taxonomic profiling using long-read sequencing technology Jean Mainguy,Olivier Bouchez,Adrien Castinel,Sylvie Combes,Christine Gaspinet al. JOBIM : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France. , 2019 Poster de conférence hal-02791605v1
Whole metagenome analysis with metagWGS Joanna Fourquet,Adeline Chaubet,Hélène Chiapello,Christine Gaspin,Marisa Haenniet al. JOBIM 2019, Jul 2019, Nantes, France. , 2019 Poster de conférence hal-02788137v1

Pré-publication, Document de travail (1)

metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads Jean Mainguy,Maïna Vienne,Joanna Fourquet,Vincent Darbot,Céline Noirotet al. 2024 Pré-publication, Document de travail hal-04841815v1

Logiciel (2)

Binette Jean Mainguy,Claire Hoede 2025, ⟨swh:1:dir:a084953ae90627320f2601b35d01620d60c16a57;origin=https://github.com/genotoul-bioinfo/Binette;visit=swh:1:snp:0843695d6f356392eaaebd39ec5f98771aa6b018;anchor=swh:1:rev:0d8d43a01383d264b92015a2f2e6ecd57350117f⟩ Logiciel hal-05058477v1
metagWGS Jean Mainguy,Maïna Vienne,Joanna Fourquet,Pierre Martin,Vincent Darbotet al. 2024, ⟨swh:1:dir:4ac81dae5fd868ea7969796dea30de32c76ff170;origin=https://hal.archives-ouvertes.fr/hal-04694918;visit=swh:1:snp:2c5d39d733f88b185b285b21578d288c1f9d9ffa;anchor=swh:1:rel:a55bc4a3ca3ff027a6ded3b1de3fb7bcff1f0bc7;path=/⟩ Logiciel hal-04694918v1