MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration
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MIntO : A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration. / Saenz, Carmen; Nigro, Eleonora; Gunalan, Vithiagaran; Arumugam, Manimozhiyan.
I: Frontiers in Bioinformatics, Bind 2, 846922, 2022.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - MIntO
T2 - A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration
AU - Saenz, Carmen
AU - Nigro, Eleonora
AU - Gunalan, Vithiagaran
AU - Arumugam, Manimozhiyan
N1 - Copyright © 2022 Saenz, Nigro, Gunalan and Arumugam.
PY - 2022
Y1 - 2022
N2 - Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome's contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.
AB - Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome's contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.
U2 - 10.3389/fbinf.2022.846922
DO - 10.3389/fbinf.2022.846922
M3 - Journal article
C2 - 36304282
VL - 2
JO - Frontiers in Bioinformatics
JF - Frontiers in Bioinformatics
SN - 2673-7647
M1 - 846922
ER -
ID: 339146571