Scalable metagenomic taxonomy classification using a reference genome database, Bioinformatics, vol.29, pp.2253-2260, 2013. ,
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences, Systematic Biology, p.54, 2018. ,
Metagenomic arbovirus detection using MinION nanopore sequencing, J. Virol. Methods, vol.249, pp.79-84, 2017. ,
Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood, Syst. Biol, vol.60, pp.291-302, 2011. ,
Aligning short reads to reference alignments and trees, Bioinformatics, vol.27, pp.2068-2075, 2011. ,
LSHPlace: fast phylogenetic placement using locality-sensitive hashing, Pac. Symp. Biocomput, pp.310-319, 2013. ,
Probiotics, gut microbiota and health, Médecine et Maladies Infectieuses, vol.44, pp.1-8, 2014. ,
Ribosomal Database Project: data and tools for high throughput rRNA analysis, Nucleic Acids Res, vol.42, pp.633-675, 2014. ,
PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy, Mol. Ecol. Resour, vol.15, pp.1435-1445, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01149047
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities, Mol. Ecol, vol.26, pp.5872-5895, 2017. ,
EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution, PLoS Biol, vol.16, issue.9, p.2005849, 2018. ,
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Appl Environ Microbiol, vol.72, issue.7, pp.5069-72, 2006. ,
The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples, J R Stat Soc Series B Stat Methodol, vol.74, pp.569-592, 2012. ,
Accelerated Profile HMM Searches, PLoS Comput. Biol, vol.7, pp.755-763, 1998. ,
Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard, vol.78, 2016. ,
Phylogenetic placement of metagenomic reads using the minimum evolution principle, Sinauer Associates, vol.16, p.13, 2003. ,
Towards a genomics-informed, real-time, global pathogen surveillance system, Nat. Rev. Genet, vol.19, pp.9-20, 2018. ,
Documenting DNA in the dust, Mol. Ecol, vol.26, pp.969-971, 2017. ,
Whole-genome sequencing in outbreak analysis, Clin. Microbiol. Rev, vol.28, pp.541-563, 2015. ,
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-328, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
Mason -A Read Simulator for Second Generation Sequencing Data, 2010. ,
Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches, Nucleic Acids Res, vol.42, pp.7-11, 2014. ,
MEGAN analysis of metagenomic data, Genome Res, vol.17, pp.377-386, 2007. ,
MEGAN Community Edition -Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data, PLoS Comput. Biol, vol.12, p.470, 2011. ,
An automated genotyping tool for enteroviruses and noroviruses, J Clin Virol, vol.51, issue.2, pp.121-126, 2011. ,
BoSSA: A Bunch of Structure and Sequence Analysis, 2018. ,
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-247, 2016. ,
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures, Bioinformatics, vol.34, pp.171-178, 2018. ,
Oxford Nanopore MinION Sequencing and Genome Assembly, Genomics Proteomics Bioinformatics, vol.14, pp.265-279, 2016. ,
Swarm: robust and fast clustering method for amplicon-based studies, PeerJ, vol.2, p.593, 2014. ,
A format for phylogenetic placements, PLoS One, vol.7, p.31009, 2012. ,
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree, BMC Bioinformatics, vol.11, p.538, 2010. ,
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison, PLoS One, vol.8, p.56859, 2013. ,
Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth, PeerJ, vol.1, p.157, 2013. ,
MetaCache: context-aware classification of metagenomic reads using minhashing, Bioinformatics, vol.33, pp.3740-3748, 2017. ,
Mash: fast genome and metagenome distance estimation using MinHash, Genome Biol, vol.17, p.132, 2016. ,
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers, BMC Genomics, vol.16, pp.313-338, 2015. ,
, , 2019.
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, vol.41, pp.590-596, 2013. ,
Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations, Nat. Rev. Genet, vol.19, p.269, 2018. ,
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics, Comput. Struct. Biotechnol. J, vol.15, pp.48-55, 2017. ,
HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly, BMC Genomics, vol.15, issue.10, p.9, 2014. ,
Unraveling the web of viroinformatics: computational tools and databases in virus research, Virol. J, vol.89, issue.3, pp.1489-501, 2018. ,
The European Nucleotide Archive in 2017, Nucleic Acids Res, vol.46, pp.36-40, 2018. ,
A communal catalogue reveals Earth's multiscale microbial diversity, Nature, vol.551, pp.457-463, 2017. ,
Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges, Crit. Rev. Clin. Lab. Sci, vol.53, pp.341-351, 2016. ,
Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biol, vol.15, p.46, 2014. ,
A new method of inference of ancestral nucleotide and amino acid sequences, Genetics, vol.141, pp.1641-1650, 1995. ,
Phylogenetic Analysis by Maximum Likelihood, Mol. Biol. Evol, vol.4, pp.1586-1591, 2007. ,
Using mobile sequencers in an academic classroom, p.5, 2016. ,