We are starting to work on an infrastructure for annotation of 16S
metagenomic sequencing datasets and would like your comments and/or
contributions. Below are links to two github repositories:
metagenomeFeatures and greengenes13.5MgDb. The metagenomeFeatures package
contains two classes; mgDb, for 16S sequence databases, and
metagenomeAnnotation, for annotating a sequence dataset with taxonomic
information from a mgDb object. The greengenes13.5MgDb package, loads a
mgDb object with the greengenes 13.5 database. greengenes 13.5 was used as
an example database, we plan on adding additional packages for other
commonly used databases, e.g RDP and Silva.
The metagenomeFeatures includes two vignettes to demonstrating the mgDb and
metagenomeAnnotation class methods using the greengenes13.5MgDb as an
example database.
We are planning on adding additional methods for the mgDb and
metagenomeAnnotation classes. For the mgDb class, assigning query
sequences to database sequences using rRDP classifier, and/or sequence
alignment methods that are part of the Biostrings package. For the
metagenomeAnnotation class we plan to include the ability to create a
phylogenetic tree from a metagenomeAnnotation object.
We would appreciate comments on the package and suggestions for additional
features.
Links to package github repositories
https://github.com/HCBravoLab/metagenomeFeatures
https://github.com/HCBravoLab/greengenes13.5MgDb
Thanks
Nate Olson and Hector Corrada Bravo
[[alternative HTML version deleted]]