metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data.

ABSTRACT

SUMMARY: We developed the metagenomeFeatures R Bioconductor package along with annotation packages for three 16S rRNA databases (Greengenes, RDP and SILVA) to facilitate working with 16S rRNA databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures for marker-gene survey feature data. The associated annotation packages provide a consistent interface to the different databases facilitating database comparison and exploration. The mgFeatures-class represents a crucial step in the development of a common data structure for working with 16S marker-gene survey data in R. AVAILABILITY AND IMPLEMENTATION https//bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html. SUPPLEMENTARY INFORMATION Supplementary material is available at Bioinformatics online.