Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
暂无分享,去创建一个
Alejandro Sanchez-Flores | Alejandra Escobar-Zepeda | Elizabeth Ernestina Godoy-Lozano | Luciana Raggi | Lorenzo Segovia | Rosa María Gutiérrez-Rios | Katy Juarez | Liliana Pardo-Lopez | Enrique Merino | Alexei F Licea-Navarro | L. Segovia | R. Gutiérrez-Ríos | K. Juárez | E. Merino | E. Godoy-Lozano | Alejandra Escobar-Zepeda | L. Pardo-López | L. Raggi | A. Licea-Navarro | A. Sánchez-Flores
[1] M. Gorzelak,et al. Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool , 2015, PloS one.
[2] Elaina D. Graham,et al. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans , 2017, Scientific Data.
[3] S. A. Boers,et al. Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures , 2015, Scientific Reports.
[4] William A. Walters,et al. QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.
[5] P. Bork,et al. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data , 2016, Molecular biology and evolution.
[6] F. Ryan,et al. SPINGO: a rapid species-classifier for microbial amplicon sequences , 2015, BMC Bioinformatics.
[7] R. Dewhurst,et al. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen , 2018, Nature Communications.
[8] Stephen J. Salipante,et al. Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling , 2014, Applied and Environmental Microbiology.
[9] Luis M Rodriguez-R,et al. A user's guide to quantitative and comparative analysis of metagenomic datasets. , 2013, Methods in enzymology.
[10] Patrick D. Schloss,et al. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system , 2016, PeerJ.
[11] B. Haas,et al. A Catalog of Reference Genomes from the Human Microbiome , 2010, Science.
[12] Hélène Touzet,et al. Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics , 2017, PloS one.
[13] Vineet K. Sharma,et al. Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes , 2016, Front. Microbiol..
[14] 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.
[15] Philip D. Blood,et al. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software , 2017, Nature Methods.
[16] Jennifer M. Fettweis,et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies , 2015, BMC Microbiology.
[17] Derrick E. Wood,et al. Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.
[18] 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.
[19] P. Baldrian,et al. The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses , 2013, PloS one.
[20] Stuart M. Brown,et al. Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes , 2010, Applied and Environmental Microbiology.
[21] Lorenzo Segovia,et al. Protein homology detection and fold inference through multiple alignment entropy profiles , 2007, Proteins.
[22] Sarah A. Butcher,et al. k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets , 2016, Nucleic acids research.
[23] Kang Ning,et al. Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization , 2014, PloS one.
[24] C. Chothia,et al. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[25] James R. Cole,et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis , 2013, Nucleic Acids Res..
[26] Pelin Yilmaz,et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..
[27] M. Martínez‐Porchas,et al. Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used , 2016, Heliyon.
[28] Peer Bork,et al. MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit , 2012, PloS one.
[29] Zhiheng Pei,et al. Pearls and pitfalls of genomics-based microbiome analysis , 2012, Emerging Microbes & Infections.
[30] N. Kyrpides,et al. Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample , 2012, PloS one.
[31] S. Lonardi,et al. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers , 2015, BMC Genomics.
[32] Paul P. Gardner,et al. An evaluation of the accuracy and speed of metagenome analysis tools , 2015, Scientific Reports.
[33] Johan Bengtsson-Palme,et al. metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data , 2015, Molecular ecology resources.
[34] Duy Tin Truong,et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling , 2015, Nature Methods.
[35] B. Matthews. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.
[36] A. Sanchez-Flores,et al. The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics , 2015, Front. Genet..
[37] Jianxin Shi,et al. Comparison of Collection Methods for Fecal Samples in Microbiome Studies , 2017, American journal of epidemiology.
[38] J. Clarridge,et al. Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases , 2004, Clinical Microbiology Reviews.
[39] Florent E. Angly,et al. Grinder: a versatile amplicon and shotgun sequence simulator , 2012, Nucleic acids research.
[40] Kang Ning,et al. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities , 2017, Scientific Reports.
[41] Eric Ravussin,et al. Impact of Different Fecal Processing Methods on Assessments of Bacterial Diversity in the Human Intestine , 2016, Front. Microbiol..
[42] Stefano Lonardi,et al. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers , 2017, Genome Biology.
[43] C. Quince,et al. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. , 2013, Environmental microbiology.
[44] Donovan H. Parks,et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life , 2017, Nature Microbiology.
[45] Steven Salzberg,et al. BIOINFORMATICS ORIGINAL PAPER , 2004 .
[46] Caleb Webber,et al. SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser , 2008, Nucleic Acids Res..