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Updated: Aug 17, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Efficient computation of contributional diversity metrics from microbiome data with FuncDiv
Gavin M Douglas1,2, Sunu Kim2, Morgan G I Langille3
1Genome Centre, McGill University, Montréal, QC H3A 0G1, Canada.
Motivation:
Microbiome datasets with taxa linked to the functions (e.g. genes) they encode are becoming more common as metagenomics sequencing approaches improve. However, these data are challenging to analyze due to their complexity. Summary metrics, such as the alpha and beta diversity of taxa contributing to each function (i.e. contributional diversity), represent one approach to investigate these data, but currently there are no straightforward methods for doing so.
Results:
We addressed this gap by developing FuncDiv, which efficiently performs these computations. Contributional diversity metrics can provide novel insights that would be impossible to identify without jointly considering taxa and functions.
Availability And Implementation:
FuncDiv is distributed under a GNU Affero General Public License v3.0 and is available at https://github.com/gavinmdouglas/FuncDiv.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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