ArticleFrontiers in bioinformatics2022
MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration.
Article in Frontiers in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Gut microbiota and tuberculosis.iMeta · 2025Review
- Article
- Article
- Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.Nature biotechnology · 2023Article
- Article
- Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.Microbiology spectrum · 2023Article
- Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori.PloS one · 2023Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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
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Registered trials
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