Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?, Fungal Ecology, vol.5, issue.6, pp.747-749, 2012. ,
DOI : 10.1016/j.funeco.2012.06.003
Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland, Microbial Ecology, vol.75, issue.2, pp.96-104, 2013. ,
DOI : 10.1007/s00248-013-0238-8
Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species, Frontiers in Zoology, vol.10, issue.1, pp.45-59, 2013. ,
DOI : 10.1111/j.1755-0998.2011.03104.x
Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring, Methods in Ecology and Evolution, vol.5, issue.4, pp.613-623, 2012. ,
DOI : 10.1111/j.2041-210X.2012.00198.x
Illumina sequencing of the V4 hypervariable region 16S rRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse, Veterinary Microbiology, vol.168, issue.2-4, pp.436-441, 2014. ,
DOI : 10.1016/j.vetmic.2013.11.017
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform, Nucleic Acids Research, vol.40, issue.1, p.3, 2012. ,
DOI : 10.1093/nar/gkr771
Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?, Molecular Ecology Resources, vol.78, issue.4, pp.620-633, 2013. ,
DOI : 10.1111/1755-0998.12103
Illumina-based analysis of microbial community diversity, The ISME Journal, vol.19, issue.1, pp.183-194, 2011. ,
DOI : 10.1038/ismej.2010.160
SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing, BMC Genomics, vol.15, issue.1, pp.110-121, 2014. ,
DOI : 10.1093/bioinformatics/btp352
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations, Nucleic Acids Research, vol.35, issue.13, p.91, 2007. ,
DOI : 10.1093/nar/gkm435
URL : http://doi.org/10.1093/nar/gkm435
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing, Cold Spring Harbor Protocols, vol.2010, issue.6, p.5448, 2010. ,
DOI : 10.1101/pdb.prot5448
URL : http://hdl.handle.net/11858/00-001M-0000-000F-F63C-C
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads, Applied and Environmental Microbiology, vol.77, issue.11, pp.3846-3852, 2011. ,
DOI : 10.1128/AEM.02772-10
PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate, Proceedings of the National Academy of Sciences, vol.111, issue.1, pp.139-148, 2013. ,
DOI : 10.1073/pnas.1317377110
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, The ISME Journal, vol.6, issue.8, pp.1621-1624, 2012. ,
DOI : 10.1038/ismej.2010.160
Modular tagging of amplicons using a single PCR for high-throughput sequencing, Molecular Ecology Resources, vol.6, issue.1, pp.117-121, 2014. ,
DOI : 10.1111/1755-0998.12162
Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification, Applied and Environmental Microbiology, vol.77, issue.21, pp.7846-7849, 2011. ,
DOI : 10.1128/AEM.05220-11
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis, Applied and Environmental Microbiology, vol.77, issue.10, pp.3219-3226, 2011. ,
DOI : 10.1128/AEM.02810-10
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing, Nature Methods, vol.7, issue.1, pp.57-59, 2012. ,
DOI : 10.1093/bioinformatics/btp636
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proceedings of the National Academy of Sciences, vol.108, issue.Supplement_1, pp.4516-4522, 2011. ,
DOI : 10.1073/pnas.1000080107
Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities, Molecular Ecology Resources, vol.30, issue.95, pp.1129-1140, 2014. ,
DOI : 10.1111/1755-0998.12261
Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit, Applied and Environmental Microbiology, vol.79, issue.21, pp.6593-6603, 2013. ,
DOI : 10.1128/AEM.00342-13
Improved Inference of Taxonomic Richness from Environmental DNA, PLoS ONE, vol.27, issue.6, p.71974, 2013. ,
DOI : 10.1371/journal.pone.0071974.s016
Molecular analyses reveal high levels of eukaryotic richness associated with enigmatic deep-sea protists (Komokiacea), Marine Biodiversity, vol.1, issue.1, pp.45-55, 2009. ,
DOI : 10.1007/s12526-009-0006-7
Molecular evidence for widespread occurrence of Foraminifera in soils, Environmental Microbiology, vol.75, issue.9, pp.2518-2526, 2010. ,
DOI : 10.1111/j.1462-2920.2010.02225.x
URL : https://hal.archives-ouvertes.fr/halsde-00525387
Novel lineages of Southern Ocean deep-sea foraminifera revealed by environmental DNA sequencing, Deep Sea Research Part II: Topical Studies in Oceanography, vol.58, issue.19-20, 1996. ,
DOI : 10.1016/j.dsr2.2011.01.009
Ancient DNA complements microfossil record in deep-sea subsurface sediments, Biology Letters, vol.104, issue.12, p.20130283, 2013. ,
DOI : 10.1073/pnas.0700520104
URL : https://hal.archives-ouvertes.fr/hal-01258222
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
On the Number of Latin Squares, Annals of Combinatorics, vol.9, issue.3, pp.335-344, 2005. ,
DOI : 10.1007/s00026-005-0261-7
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, Nucleic Acids Research, vol.41, issue.D1, pp.597-604, 2013. ,
DOI : 10.1093/nar/gks1160
URL : https://hal.archives-ouvertes.fr/hal-01253994
UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, issue.16, pp.2194-2200, 2011. ,
DOI : 10.1093/bioinformatics/btr381
A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies, BMC Genomics, vol.11, issue.1, pp.296-310, 2010. ,
DOI : 10.1186/1471-2164-11-296
URL : https://hal.archives-ouvertes.fr/lirmm-00487231
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform, Applied and Environmental Microbiology, vol.79, issue.17, pp.5112-5120, 2013. ,
DOI : 10.1128/AEM.01043-13
Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses, Nucleic Acids Research, vol.40, issue.9, p.66, 2012. ,
DOI : 10.1093/nar/gks002
Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces, PLoS ONE, vol.114, issue.10, p.56335, 2013. ,
DOI : 10.1371/journal.pone.0056335.s009
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities, Environmental Microbiology, vol.6, issue.Suppl 1, 2013. ,
DOI : 10.1111/1462-2920.12250
URL : https://hal.archives-ouvertes.fr/hal-01258219
Experimental factors affecting PCR-based estimates of microbial species richness and evenness, The ISME Journal, vol.62, issue.5, pp.642-647, 2010. ,
DOI : 10.1128/AEM.00592-09
Illumina metabarcoding of a soil fungal community, Soil Biology and Biochemistry, vol.65, pp.128-132, 2013. ,
DOI : 10.1016/j.soilbio.2013.05.014
Groundtruthing Next-Gen Sequencing for Microbial Ecology???Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing, PLoS ONE, vol.7, issue.9, p.44224, 2012. ,
DOI : 10.1371/journal.pone.0044224.s006
A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust, Microbial Ecology, vol.14, issue.4, pp.735-741, 2013. ,
DOI : 10.1007/s00248-013-0266-4
Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing, Applied and Environmental Microbiology, vol.76, issue.12, pp.3863-3868, 2010. ,
DOI : 10.1128/AEM.02585-09
The role of replicates for error mitigation in next-generation sequencing, Nature Reviews Genetics, vol.802, issue.1, pp.56-62, 2014. ,
DOI : 10.1186/gb-2007-8-7-r143
Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities, PLoS ONE, vol.304, issue.2, p.29973, 2012. ,
DOI : 10.1371/journal.pone.0029973.t004
High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities, Methods in Ecology and Evolution, vol.8, issue.6, pp.558-565, 2013. ,
DOI : 10.1111/2041-210X.12037
454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes, PLoS ONE, vol.21, issue.8, p.74371, 2013. ,
DOI : 10.1371/journal.pone.0074371.s008
URL : https://hal.archives-ouvertes.fr/hal-01258226
Reproducibility and quantitation of amplicon sequencing-based detection, The ISME Journal, vol.62, issue.8, pp.1303-1313, 2011. ,
DOI : 10.1073/pnas.0709016105
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins, Proceedings of the National Academy of Sciences, vol.107, issue.16, pp.7503-7508, 2010. ,
DOI : 10.1073/pnas.1002355107
Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens, Molecular Ecology Resources, vol.7, issue.Suppl S1, pp.892-901, 2014. ,
DOI : 10.1111/1755-0998.12236