MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data.

In microbiome research, metagenomic sequencing generates enormous amounts of data. These data are typically classified into taxa for taxonomy analysis, or into genes for functional analysis. However, a joint analysis where the reads are classified into taxa-specific genes is often overlooked. To enable the analysis of this biologically meaningful feature, we developed a novel bioinformatic toolkit, MetaPrism, which can analyze sequence reads for a set of joint taxa/gene analyses to: 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) compare the abundances between groups; and 4) build prediction models for clinical outcome. We illustrated these functions using a published microbiome metagenomics dataset from patients treated with immune checkpoint inhibitor therapy and showed the joint features can serve as potential biomarkers to predict therapeutic responses. MetaPrism is a toolkit for joint taxa and gene analysis. It offers biological insights on the taxa-specific genes on top of the taxa-alone or gene-alone analysis. MetaPrism is open-source software and freely available at https://github.com/jiwoongbio/MetaPrism. The example script to reproduce the manuscript is also provided in the above code repository. © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

Citation

Jiwoong Kim, Shuang Jiang, Yiqing Wang, Guanghua Xiao, Yang Xie, Dajiang J Liu, Qiwei Li, Andrew Koh, Xiaowei Zhan. MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data. G3 (Bethesda, Md.). 2021 Apr 15;11(4)

PMID: 33713107

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