[Bioc-devel] Request for comment metagenomeFeatures package

Martin Morgan mtmorgan at fredhutch.org
Tue Aug 4 21:00:12 CEST 2015

On 08/04/2015 06:43 AM, Nathan Olson wrote:
> 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

does it make sense to use AnnotationHub to manage these resources? Instead of 
downloading and managing the fasta and taxonomy files in .onLoad and 
getGreenGenes13.5Db, .onLoad would be

   hub = AnnotationHub()
   db_seq = hub[["AH12345"]]
   db_taxa_file = hub[["AH12346"]]

with a 'recipe' describing how the corresponding annotation hub resources are to 
be created. This would move download and management to AnnotationHub, and 
potentially allow use of the annotation hub records by people with other 
interests. If that sounds interesting we can work up a pull request.


> 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

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