A clinician's guide to microbiome analysis

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Search and clustering orders of magnitude faster than BLAST

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

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Pfam: the protein families database

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Quality control and preprocessing of metagenomic datasets

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Richness of human gut microbiome correlates with metabolic markers

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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

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The COG database: an updated version includes eukaryotes

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Coming of age: ten years of next-generation sequencing technologies

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Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR ampliconsPreprint

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Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

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Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk

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Gut microbiota composition correlates with diet and health in the elderly

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The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

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IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

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Personalized nutrition by prediction of glycemic responses

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NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

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Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

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Differential abundance analysis for microbial marker-gene surveys

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The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

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MetaPhlAn2 for enhanced metagenomic taxonomic profiling

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

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eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

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Human gut microbes impact host serum metabolome and insulin sensitivity

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InterPro: the integrative protein signature database

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Fast and sensitive taxonomic classification for metagenomics with Kaiju

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The RDP (Ribosomal Database Project)

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MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

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Ab initio gene identification in metagenomic sequences

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MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

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Antibiotics in early life alter the murine colonic microbiome and adiposity

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The Application of Ecological Theory Toward an Understanding of the Human Microbiome

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Topographic diversity of fungal and bacterial communities in human skin

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The gut microbiota in IBD

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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

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The vocabulary of microbiome research: a proposal

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Microbes, Microbiota, and Colon Cancer

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Tumour-associated and non-tumour-associated microbiota in colorectal cancer

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MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

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How to apply de Bruijn graphs to genome assembly

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Gene and translation initiation site prediction in metagenomic sequences

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eggNOG v4.0: nested orthology inference across 3686 organisms

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CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

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Swarm v2: highly-scalable and high-resolution amplicon clustering

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Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons

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Ray Meta: scalable de novo metagenome assembly and profiling

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Metagenomic Pyrosequencing and Microbial Identification

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Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

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Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

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Sample storage conditions significantly influence faecal microbiome profiles

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Metagenomic species profiling using universal phylogenetic marker genes

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Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

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Compilation of small ribosomal subunit RNA structures

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CAMERA: A Community Resource for Metagenomics

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