shahnidhi / silva123.1mgdb Goto Github PK

This is a Bioconductor Annotation package with the SILVA SSU RNA database Version 123.1 for use with 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/silva123.1MgDb.git`
3. download the database sequence data from `inst/scripts` using `get_silva12.1MgDb.R` script to generate the metadata and database file required for the silva123.1MgDb.

4. install silva123.1, this can be done using devtools `install_local("local/path/silva123.1MgDb")`, replace `local/path` with the path to the downloaded git repo.

The metagenomeFeatures package has vignettes demonstrating how to work with MgDb-class formated sequence databases.