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Metagenomic Datasets Simulated In Silico for the Evaluation of Nonpareil

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https://hdl.handle.net/1853/71004
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2014 14
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Low Richness -- Set 1

2014-02-03 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

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Escherichia Genomes -- Set 2

2014-02-03 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

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Escherichia Genomes -- Set 1

2014-01-31 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

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Escherichia Genomes -- Set 4

2014-01-31 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

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All Complete Bacterial and Archeal Genomes -- Set 6

2014-02-03 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

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All Complete Bacterial and Archeal Genomes -- Set 7

2014-02-03 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

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Item

Escherichia Genomes -- Set 6

2014-01-31 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

View
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Item

All Complete Bacterial and Archeal Genomes -- Set 3

2014-02-03 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

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Item

Low Richness -- Set 2

2014-02-03 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

View
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Item

All Complete Bacterial and Archeal Genomes -- Set 5

2014-01-31 , Konstantinidis, Kostas T. , Rodriguez, Luis M.

Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Due to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, OTU calling, or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.

View