SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012. ,
DOI : 10.1089/cmb.2012.0021
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/pdf
Ribosomal Database Project: data and tools for high throughput rRNA analysis, Nucleic Acids Research, vol.4, issue.D1, pp.42-633, 2014. ,
DOI : 10.1128/AEM.01043-13
URL : https://academic.oup.com/nar/article-pdf/42/D1/D633/16952330/gkt1244.pdf
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB, Applied and Environmental Microbiology, vol.72, issue.7, pp.72-5069, 2006. ,
DOI : 10.1128/AEM.03006-05
SeqAn An efficient, generic C++ library for sequence analysis, BMC Bioinformatics, vol.9, issue.1, pp.1-9, 2008. ,
DOI : 10.1186/1471-2105-9-11
UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.63, issue.Pt 5, pp.27-2194, 2011. ,
DOI : 10.1099/13500872-142-5-1107
Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms, Nucleic Acids Research, vol.6, issue.10, pp.4504-4518, 2016. ,
DOI : 10.1093/bioinformatics/bts597
ART: a next-generation sequencing read simulator, Bioinformatics, vol.3, issue.4, pp.593-594, 2012. ,
DOI : 10.1371/journal.pone.0003373
URL : https://academic.oup.com/bioinformatics/article-pdf/28/4/593/16911715/btr708.pdf
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, vol.2, issue.24, pp.28-3211, 2012. ,
DOI : 10.3389/fmicb.2011.00134
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
ABSTRACT, mSystems, vol.1, issue.1, 2016. ,
DOI : 10.1128/mSystems.00003-15
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, vol.464, issue.10, pp.31-1674, 2015. ,
DOI : 10.1038/nature08821
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences, BMC Genomics, issue.2, pp.12-16, 2011. ,
Scaling laws predict global microbial diversity, Proceedings of the National Academy of Sciences, pp.5970-5975, 2016. ,
DOI : 10.1073/pnas.1521291113
URL : http://www.pnas.org/content/113/21/5970.full.pdf
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, issue.1, pp.10-12, 2011. ,
DOI : 10.14806/ej.17.1.200
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods, Nature Methods, vol.22, issue.6, pp.495-500, 2007. ,
DOI : 10.1093/oxfordjournals.molbev.a026048
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes, Nucleic Acids Research, vol.42, issue.D1, pp.45-529, 2017. ,
DOI : 10.1093/nar/gkw290
Sumatra and sumaclust: fast and exact comparison and clustering of sequences, 2013. ,
MetaQUAST: evaluation of metagenome assemblies, Bioinformatics, vol.7, issue.7, pp.1088-1090, 2016. ,
DOI : 10.1093/nar/gkq275
URL : https://academic.oup.com/bioinformatics/article-pdf/32/7/1088/19568745/btv697.pdf
Infernal 1.0: inference of RNA alignments, Bioinformatics, issue.10, pp.25-1335, 2009. ,
metaSPAdes: a new versatile metagenomic assembler, Genome Research, vol.5, issue.5, 2016. ,
DOI : 10.1101/gr.074492.107
URL : http://doi.org/10.1101/gr.213959.116
Interactive metagenomic visualization in a Web browser, BMC Bioinformatics, vol.12, issue.1, p.385, 2011. ,
DOI : 10.1038/nature08821
URL : http://doi.org/10.1186/1471-2105-12-385
Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data, PLoS ONE, vol.5, issue.5, p.19984, 2011. ,
DOI : 10.1371/journal.pone.0019984.s008
Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics, PLoS ONE, vol.6, issue.4, p.93827, 2014. ,
DOI : 10.1371/journal.pone.0093827.s001
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, vol.35, issue.D1, pp.41-590, 2013. ,
DOI : 10.1093/nar/gkl856
URL : https://academic.oup.com/nar/article-pdf/41/D1/D590/3690367/gks1219.pdf
VSEARCH: a versatile open source tool for metagenomics, PeerJ, vol.4, 2016. ,
DOI : 10.7287/peerj.preprints.2409
URL : https://doi.org/10.7287/peerj.preprints.2409
Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.11, issue.5, pp.863-864, 2011. ,
DOI : 10.1111/j.1462-2920.2009.01901.x
Critical Assessment of Metagenome Interpretation -a benchmark of computational metagenomics software, p.99127, 2017. ,
DOI : 10.1101/099127
URL : https://hal.archives-ouvertes.fr/hal-01633525
Metagenomic microbial community profiling using unique clade-specific marker genes, Nature Methods, vol.2008, issue.8, pp.9-811, 2012. ,
DOI : 10.1093/nar/gkn879
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443552/pdf
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities, Environmental Microbiology, vol.5, issue.Suppl. 2, pp.15-1882, 2013. ,
DOI : 10.1038/ismej.2011.11
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665634/pdf
Efficient de novo assembly of large genomes using compressed data structures, Genome Research, vol.22, issue.3, pp.549-556, 2012. ,
DOI : 10.1101/gr.126953.111
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy, Applied and Environmental Microbiology, issue.16, pp.73-5261, 2007. ,
Reconstructing 16S rRNA genes in metagenomic data, Bioinformatics, vol.31, issue.12, pp.31-35, 2015. ,
DOI : 10.1371/journal.pcbi.1003737
URL : https://academic.oup.com/bioinformatics/article-pdf/31/12/i35/570626/btv231.pdf