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Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Fast and accurate short read alignment with Burrows–Wheeler transform
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PyNAST: a flexible tool for aligning sequences to a template alignment
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Fast and accurate long-read alignment with Burrows–Wheeler transform
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PBSIM: PacBio reads simulator—toward accurate genome assembly
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Omega: an Overlap-graphde novoAssembler for Metagenomics
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msa: an R package for multiple sequence alignment
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MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
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Pseudoalignment for metagenomic read assignment
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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
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How Close Is Close: 16S rRNA Sequence Identity May Not Be Sufficient To Guarantee Species Identity
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Nocardia paucivorans sp. nov.
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Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
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SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences
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UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
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Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins
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Regression Shrinkage and Selection Via the Lasso
inferredcites →https://doi.org/10.1126/science.1132690openalex-snapshot
Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis
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Optimization by Simulated Annealing
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample
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16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
inferredcites →https://doi.org/10.1128/msystems.00191-16openalex-snapshot
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
inferredcites →https://doi.org/10.1136/gutjnl-2012-303954openalex-snapshot
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inferredcites →https://doi.org/10.1186/1471-2105-12-271openalex-snapshot
DNACLUST: accurate and efficient clustering of phylogenetic marker genes
inferredcites →https://doi.org/10.1186/1471-2105-13-283openalex-snapshot
Denoising PCR-amplified metagenome data
inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
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Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform
inferredcites →https://doi.org/10.1186/2049-2618-2-31openalex-snapshot
16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles
inferredcites →https://doi.org/10.1186/gb-2011-12-2-r18openalex-snapshot
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
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Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
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Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
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Obesity, fatty liver disease and intestinal microbiota
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A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data
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A note on the group lasso and a sparse group lasso
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MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
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Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1186/s40168-018-0569-2openalex-snapshot
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
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