Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
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Aleksandra Tarkowska | Robert D Finn | R. Finn | Aleksandra Tarkowska | A. Mitchell | Alexandre Almeida | Alexandre Almeida | Alex L Mitchell
[1] Pelin Yilmaz,et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks , 2013, Nucleic Acids Res..
[2] Philip D. Blood,et al. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software , 2017, Nature Methods.
[3] William A. Walters,et al. QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.
[4] Patrick D. Schloss,et al. Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies , 2011, PloS one.
[5] Rick L. Stevens,et al. A communal catalogue reveals Earth’s multiscale microbial diversity , 2017, Nature.
[6] C. Quince,et al. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. , 2013, Environmental microbiology.
[7] Martin Hartmann,et al. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.
[8] N. Segata,et al. Shotgun metagenomics, from sampling to analysis , 2017, Nature Biotechnology.
[9] Jennifer M. Fettweis,et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies , 2015, BMC Microbiology.
[10] Susan Holmes,et al. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.
[11] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[12] Leping Li,et al. ART: a next-generation sequencing read simulator , 2012, Bioinform..
[13] Patrick D. Schloss,et al. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system , 2016, PeerJ.
[14] Robert D. Finn,et al. EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies , 2017, Nucleic Acids Res..
[15] J. Palmer,et al. Investigating Deep Phylogenetic Relationships among Cyanobacteria and Plastids by Small Subunit rRNA Sequence Analysis 1 , 1999, The Journal of eukaryotic microbiology.
[16] N. Fierer. Embracing the unknown: disentangling the complexities of the soil microbiome , 2017, Nature Reviews Microbiology.
[17] N. Pace,et al. The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences , 1986 .
[18] G. Van Domselaar,et al. The Gut Microbiota in Immune-Mediated Inflammatory Diseases , 2016, Front. Microbiol..
[19] Rafael A. Irizarry,et al. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses , 2017, Nature Communications.
[20] Jonathan L. Golob,et al. Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities , 2017, BMC Bioinformatics.
[21] E. Mardis,et al. An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.
[22] Paul P. Gardner,et al. An evaluation of the accuracy and speed of metagenome analysis tools , 2015, Scientific Reports.
[23] D. Huson,et al. SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? , 2017, BMC Genomics.
[24] Pelin Yilmaz,et al. Expanding the World of Marine Bacterial and Archaeal Clades , 2016, Front. Microbiol..
[25] G. Douglas,et al. Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research , 2017, mSystems.
[26] C. Elwood,et al. Design and Performance of a 16S rRNA-Targeted Oligonucleotide Probe for Detection of Members of the Genus Bdellovibrio by Fluorescence In Situ Hybridization , 2007, Applied and Environmental Microbiology.
[27] Sarah L. Westcott,et al. Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform , 2013, Applied and Environmental Microbiology.
[28] M. Watson,et al. The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies , 2018, Applied and Environmental Microbiology.
[29] Christian von Mering,et al. MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis , 2017, Bioinform..
[30] James R. Cole,et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis , 2013, Nucleic Acids Res..
[31] Scott Federhen,et al. The NCBI Taxonomy database , 2011, Nucleic Acids Res..
[32] Elizabeth M Glass,et al. MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. , 2016, Methods in molecular biology.
[33] Graziano Pesole,et al. BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS , 2015, BMC Bioinformatics.
[34] Rob Knight,et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin , 2018, Microbiome.
[35] Yong Wang,et al. Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis , 2016, BMC Bioinformatics.
[36] Eric P. Nawrocki,et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.
[37] A. Klindworth,et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.
[38] Karen P. Scott,et al. 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice , 2015, Microbiome.
[39] J. Tiedje,et al. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.