R: (Data) Global patterns of 16S rRNA diversity at a depth of...
data-GlobalPatterns
R Documentation
(Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)
Description
Published in PNAS in early 2011. This work compared the microbial
communities from 25 environmental samples and three known “mock communities”
– a total of 9 sample types – at a depth averaging 3.1 million reads per sample.
Authors were able to reproduce diversity patterns seen in many other
published studies, while also invesitigating technical issues/bias by
applying the same techniques to simulated microbial communities of known
composition.
Details
abstract from research article (quoted):
The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
(end quote)
Many thanks to J. Gregory Caporaso for directly providing the OTU-clustered data files
for inclusion in this package.
Author(s)
Caporaso, J. G., et al.
References
Caporaso, J. G., et al. (2011).
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.
PNAS, 108, 4516-4522.
PMCID: PMC3063599
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(phyloseq)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/phyloseq/data-GlobalPatterns.Rd_%03d_medium.png", width=480, height=480)
> ### Name: data-GlobalPatterns
> ### Title: (Data) Global patterns of 16S rRNA diversity at a depth of
> ### millions of sequences per sample (2011)
> ### Aliases: GlobalPatterns data-GlobalPatterns
> ### Keywords: data
>
> ### ** Examples
>
> data(GlobalPatterns)
> plot_richness(GlobalPatterns, x="SampleType", measures=c("Observed", "Chao1", "Shannon"))
Warning message:
Removed 52 rows containing missing values (geom_errorbar).
>
>
>
>
>
> dev.off()
null device
1
>