Software Notes:
Motivation: Next-generation sequencing, and particularly 16S ribosomal RNA (16S rRNA) gene sequencing, is a powerful technique for the identification and quantification of human-resident microbes, collectively known as the human microbiota. Once bacterial abundances are profiled via 16S rRNA gene sequencing and summarized in a count data set, diversity indices provide valuable mathematical tools to investigate the composition of the human microbiota. In brief, alpha diversity can be used to describe the taxonomical complexity of a single sample, whereas beta diversity can be used to identify differences between samples.
Results: The DiversitySeq package implements in a unified framework the whole panel of diversity indices reviewed in (Finotello et al., 2016), enabling the assessment of diversity from count data sets. DiversitySeq also implements a simulator for the generation of synthetic count data sets from 16S rRNA gene sequencing. Besides 16S rRNA gene sequencing data, this package can be employed with other data sets with similar characteristics, such as 5S rRNA gene sequencing, environmental metagenomics or, more generally, any kind of matrix were counts are computed for different non-overlapping classes.
Citation
If you use the software for your research, please refer to the original DiversitySeq paper with the citation below.
Finotello F, Mastrorilli E, Di Camillo B. Measuring the diversity of the human microbiota with targeted next-generation sequencing. Briefings in Bioinformatics. 2018 Jul; 19(4):679-692.
