Host-microbiota interactions: from holobiont theory to analysis, vol.7, p.5, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-01980500
Host-microbe interactions in octocoral holobionts: recent advances and perspectives, p.64, 2018. ,
Insights into flagellar function and mechanism from the squid-vibrio symbiosis, npj Biofilms Microbiomes, vol.5, p.32, 2019. ,
The terrestrial isopod microbiome: an all-in-one toolbox for animal-microbe interactions of ecological relevance, Front. Microbiol, vol.7, p.1472, 2016. ,
Genomics and evolution of heritable bacterial symbionts, Annu. Rev. Genet, vol.42, pp.165-190, 2008. ,
The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity, IUBMB life, vol.63, pp.1068-1074, 2011. ,
BlobTools: interrogation of genome assemblies, 1000. ,
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes, Nucleic Acids Res, vol.47, p.57, 2019. ,
metaSPAdes: a new versatile metagenomic assembler, Genome Res, vol.27, pp.824-834, 2017. ,
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, vol.28, pp.1420-1428, 2012. ,
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, vol.31, pp.1674-1676, 2015. ,
Critical assessment of metagenome interpretation: a benchmark of metagenomics software, Nat. Methods, vol.14, pp.1063-1071, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01633525
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads: a baiting and iterative mapping approach, Nucleic Acids Res, vol.41, p.129, 2013. ,
NOVOPlasty: de novo assembly of organelle genomes from whole genome data, Nucleic Acids Res, vol.45, p.18, 2017. ,
LOCAS: a low coverage assembly tool for resequencing projects, PLoS One, vol.6, p.23455, 2011. ,
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement, PLoS One, vol.9, p.112963, 2014. ,
Multiple reference genomes and transcriptomes for Arabidopsis thaliana, Nature, vol.477, pp.419-423, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00909088
MetaCompass: reference-guided assembly of metagenomes, 2017. ,
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009. ,
Space-efficient and exact de Bruijn graph representation based on a Bloom filter, Algorithms Mol. Biol, vol.8, p.22, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00868805
MindTheGap: integrated detection and assembly of short and long insertions, Bioinformatics, vol.30, pp.3451-3457, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01087832
GATB: genome assembly & analysis tool box, Bioinformatics, vol.30, pp.2959-2961, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01088571
Bandage: interactive visualization of de novo genome assemblies, Bioinformatics, vol.31, pp.3350-3352, 2015. ,
Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches, p.181, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01638839
Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola, Mol. Phylogenet. Evol, vol.68, pp.42-54, 2013. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens, Anal. Methods, vol.8, pp.12-24, 2016. ,
QUAST: quality assessment tool for genome assemblies, Bioinformatics, vol.29, pp.1072-1075, 2013. ,
Genome graphs and the evolution of genome inference, Genome Res, vol.27, pp.665-676, 2017. ,
, Computational pan-genomics: status, promises and challenges, The Computational Pan-Genomics Consortium, vol.19, pp.118-135, 2018.
Variation graph toolkit improves read mapping by representing genetic variation in the reference, Nat. Biotechnol, vol.36, pp.875-879, 2018. ,
Bit-parallel sequence-to-graph alignment, Bioinformatics, vol.35, pp.3599-3607, 2019. ,