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

ABSTRACT: 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.

SUBMITTER: Kim J

PROVIDER: S-EPMC8049424 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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

Kim Jiwoong J Jiang Shuang S Wang Yiqing Y Xiao Guanghua G Xie Yang Y Liu Dajiang J DJ Li Qiwei Q Koh Andrew A Zhan Xiaowei X

G3 (Bethesda, Md.) 20210401 4

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 ...[more]

PMID: 33713107

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Project description:BackgroundWhile next-generation sequencing (NGS) technologies are rapidly advancing, an area that lags behind is the development of efficient and user-friendly tools for preliminary analysis of massive NGS data. As an effort to fill this gap to keep up with the fast pace of technological advancement and to accelerate data-to-results turnaround, we developed a novel software package named SeqAssist ("Sequencing Assistant" or SA).ResultsSeqAssist takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data. It consists of three separate workflows: (1) the SA_RunStats workflow generates basic statistics about an NGS dataset, including numbers of raw, cleaned, redundant and unique reads, redundancy rate, and a list of unique sequences with length and read count; (2) the SA_Run2Ref workflow estimates the breadth, depth and evenness of genome-wide coverage of the NGS dataset at a nucleotide resolution; and (3) the SA_Run2Run workflow compares two NGS datasets to determine the redundancy (overlapping rate) between the two NGS runs. Statistics produced by SeqAssist or derived from SeqAssist output files are designed to inform the user: whether, what percentage, how many times and how evenly a genomic locus (i.e., gene, scaffold, chromosome or genome) is covered by sequencing reads, how redundant the sequencing reads are in a single run or between two runs. These statistics can guide the user in evaluating the quality of a DNA library prepared for RNA-Seq or genome (re-)sequencing and in deciding the number of sequencing runs required for the library. We have tested SeqAssist using a synthetic dataset and demonstrated its main features using multiple NGS datasets generated from genome re-sequencing experiments.ConclusionsSeqAssist is a useful and informative tool that can serve as a valuable "assistant" to a broad range of investigators who conduct genome re-sequencing, RNA-Seq, or de novo genome sequencing and assembly experiments.

Dataset Information

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

Publications

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

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