SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, vol.19, pp.455-477, 2012. ,
Ribosomal Database Project: data and tools for high throughput rRNA analysis, Nucleic Acids Res, vol.42, pp.633-642, 2014. ,
Greengenes, a chimera-checked 16s rRNA gene database and workbench compatible with ARB, Appl. Environ. Microbiol, vol.72, pp.5069-5072, 2006. ,
Seqan an efficient, generic c þþ library for sequence analysis, BMC Bioinformatics, vol.9, pp.1-9, 2008. ,
UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, pp.2194-2200, 2011. ,
Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms, Nucleic Acids Res, vol.44, pp.4504-4518, 2016. ,
ART: a next-generation sequencing read simulator, Bioinformatics, vol.28, pp.593-594, 2012. ,
Sortmerna: fast and accurate filtering of ribosomal rnas in metatranscriptomic data, Bioinformatics, vol.28, pp.3211-3217, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00748990
Sortmerna 2: ribosomal rna classification for taxonomic assignation, Workshop on Recent Computational Advances in Metagenomics, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01094011
Open-source sequence clustering methods improve the state of the art. mSystems, vol.1, pp.3-15, 2016. ,
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. ,
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences, BMC Genomics, vol.12, p.4, 2011. ,
Scaling laws predict global microbial diversity, Proc. Natl. Acad. Sci. USA, vol.113, pp.5970-5975, 2016. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, pp.10-12, 2011. ,
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods, Nat. Methods, vol.4, pp.495-500, 2007. ,
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes, Nucleic Acids Res, vol.45, pp.529-534, 2017. ,
SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences, Programs and Abstracts of the SeqBio 2013 workshop. Abstract, pp.27-29, 2013. ,
MetaQUAST: evaluation of metagenome assemblies, Bioinformatics, vol.32, pp.1088-1090, 2016. ,
Emirge: reconstruction of full-length ribosomal genes from microbial community short read sequencing data, Genome Biol, vol.12, p.44, 2011. ,
Infernal 1.0: inference of RNA alignments, Bioinformatics, vol.25, pp.1335-1337, 2009. ,
, metaSPAdes: a new versatile de novo metagenomics assembler, 2016.
Interactive metagenomic visualization in a Web browser, BMC Bioinformatics, vol.12, p.385, 2011. ,
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data, Plos One, vol.6, p.19984, 2011. ,
Strengths and limitations of 16s rRNA gene amplicon sequencing in revealing temporal microbial community dynamics, PLoS ONE, vol.9, p.93827, 2014. ,
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, vol.41, pp.590-596, 2013. ,
VSEARCH: a versatile open source tool for metagenomics, 2016. ,
Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-864, 2011. ,
Critical assessment of metagenome interpretation -a benchmark of computational metagenomics software. bioRxiv, p.99127, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01633525
Metagenomic microbial community profiling using unique clade-specific marker genes, Nat. Methods, vol.9, pp.811-814, 2012. ,
Comparative metagenomic and rRNA microbial diversity characterization using Archaeal and Bacterial synthetic communities, Environ. Microbiol, vol.15, pp.1882-1899, 2013. ,
Efficient de novo assembly of large genomes using compressed data structures, Genome Res, vol.22, pp.549-556, 2012. ,
, The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome, Nature, vol.486, pp.207-214
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol, vol.73, pp.5261-5267, 2007. ,
Reconstructing 16s rRNA genes in metagenomic data, Bioinformatics, vol.31, pp.35-43, 2015. ,
, Human mouth sample SRS016002. % identity distribution of best matches against Silva 128 SSU Ref NR