Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples

TL;DR

Thanos is an R package that simplifies analyzing the functional potential of microbial communities in metagenomic data.

Contribution

Thanos introduces a streamlined, user-friendly R package for pathway-centric analysis of metagenomic functional potential.

Findings

Thanos enables quantitative analysis of prevalent metabolic pathways in microbial communities.

The package supports comparison of functional potential across different environments.

It provides visualization tools like bar plots and annotated pathway graphs for results.

Abstract

As the amount of metagenomic sequencing continues to increase, there is a growing need for tools that help biologists make sense of the data. Specifically, researchers are often interested in the potential of a microbial community to carry out a metabolic reaction, but this analysis requires knitting together multiple software tools into a complex pipeline. Thanos offers a user-friendly R package designed for the pathway-centric analysis and visualization of the functions encoded within metagenomic samples. It allows researchers to go beyond taxonomic profiles and find out, quantitatively, which pathways are prevalent in an environment, as well as comparing different environments in terms of their functional potential. The analysis is based on the sequencing depth of the genes of interest, either in the metagenome-assembled genomes (MAGs) or in the assembled reads (contigs), using a normalization strategy that enables comparison across samples. The package can import the data from multiple formats and offers functions for the visualization of the results as bar plots of the functional profile, box plots of compare functions across samples, and annotated pathway graphs. By streamlining the analysis of the functional potential encoded in microbial communities, Thanos can enable impactful discoveries in all the fields touched by metagenomics, from human health to the environmental sciences.

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