Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods (Q39198664)

9 September 2017

Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods (English)

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9 September 2017

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9 September 2017

1 March 2016

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9 September 2017

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9 September 2017

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9 September 2017

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NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Limits to robustness and reproducibility in the demarcation of operational taxonomic units

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

A comparison of methods for clustering 16S rRNA sequences into OTUs

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

UPARSE: highly accurate OTU sequences from microbial amplicon reads

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Stabilization of the murine gut microbiome following weaning

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

QIIME allows analysis of high-throughput community sequencing data

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Alignment and clustering of phylogenetic markers--implications for microbial diversity studies

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Pyrosequencing enumerates and contrasts soil microbial diversity

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

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

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Swarm: robust and fast clustering method for amplicon-based studies

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Comparing clustering and pre-processing in taxonomy analysis

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5069744

Open-Source Sequence Clustering Methods Improve the State Of the Art.

21 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27832214

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/MSYSTEMS.00027-16

0 references

PMCID

5069744

1 reference

9 September 2017

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PMCID

5069744