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:
-
install metagenomeFeatures, this can be done using devtools
install_github("HCBravoLab/metagenomeFeatures")
-
clone this repository
git clone https://github.com/HCBravoLab/greengenes13.8OTU97MgDb.git
-
to download the database data, from the
inst/scripts
directory in the repository run theget_greengenes13.8OTU97MgDb.R
script. Note the script requiresdplyr
,RSQLite
,phyloseq
, andBiostrings
. -
install greengenes13.8OTU97MgDb, this can be done using devtools
install_local("local/path/greengenes13.8OTU97MgDb")
, replacelocal/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.