README.md

In daniel01001000/greengenes13.8_97MgDb: Greengenes 13.8 97% similarity OTU threshold 16S rRNA Database Annotation Data

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.

1. install greengenes13.8OTU97MgDb, this can be done using devtools 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.

daniel01001000/greengenes13.8_97MgDb documentation built on May 14, 2019, 3:40 p.m.