ArticleGenome biology2016
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.Nature communications · 2026Article
- Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.mSphere · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.Microbiome · 2025Article
- Computational Metagenomics: State of the Art.International journal of molecular sciences · 2025Review
- Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.NPJ biofilms and microbiomes · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.BMC bioinformatics · 2025Article
- Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science.Metabolites · 2025Review
- Ketogenic diet suppresses colorectal cancer through the gut microbiome long chain fatty acid stearate.Nature communications · 2025Article
- Predicting climate-change impacts on the global glacier-fed stream microbiome.Nature communications · 2025Article
- Article
- Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.ISME communications · 2025Article
- Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome.Nature microbiology · 2025Article
- Personalized modeling of gut microbiome metabolism throughout the first year of life.Communications medicine · 2024Article
- gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes.GigaScience · 2024Article
- Forecasting the dynamics of a complex microbial community using integrated meta-omics.Nature ecology & evolution · 2024Article
- Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data.Briefings in bioinformatics · 2023Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.