This is an R package with the greengenes 13.8 database 97 similarty cutoff OTU set for annotating 16S metagenomic sequence data using the metagenomeFeatures package (https://github.com/HCBravoLab/metagenomeFeatures.git).
The package is still in development and not available from bioconductor.
To install the development version of the package:
1. install metagenomeFeatures, this can be done using devtools install_github("HCBravoLab/metagenomeFeatures")
2. clone this repository git clone https://github.com/HCBravoLab/greengenes13.8OTU97MgDb.git
3. to download the database data, from the inst/scripts
directory in the repository run the get_greengenes13.8OTU97MgDb.R
script. Note the script requires dplyr
, RSQLite
, phyloseq
, and Biostrings
.
install_local("local/path/greengenes13.8OTU97MgDb")
, replace local/path
with the path to the downloaded git repo. The metagenomeFeatures package has vignettes demonstrating how to use the greenegenes13.8OTU97MgDb package to annotate 16S rRNA metagenomic sequence data.
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