ArticleScientific reports2016
MetaTrans: an open-source pipeline for metatranscriptomics.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults.The Journal of nutritional biochemistry · 2020Trial
- DeepCYP: an integrated deep learning web server for the holistic "pathway-site product" prediction of CYP450 metabolism.Nucleic acids research · 2026Article
- Interpreting fungal ecological contributions through taxonomic and functional profiling of metatranscriptomics.IMA fungus · 2026Review
- Species-specific rumen microbial responses to dietary inhibition of methanogenesis in cows and goats.Frontiers in microbiology · 2026Article
- Rumen microbiota associated with feed efficiency in beef cattle are highly influenced by diet composition.Animal nutrition (Zhongguo xu mu shou yi xue hui) · 2025Article
- metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.BMC bioinformatics · 2025Article
- Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.Journal of microbiology and biotechnology · 2025Review
- Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science.Metabolites · 2025Review
- Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.ISME communications · 2025Article
- Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil.3 Biotech · 2023Review
- Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes.BMC microbiology · 2023Article
- MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities.Microbiome · 2023Article
- The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in bioinformatics · 2023Article
- Metatranscriptomic analysis of the gut microbiome of black soldier fly larvae reared on lignocellulose-rich fiber diets unveils key lignocellulolytic enzymes.Frontiers in microbiology · 2023Article
- Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response.Molecular biology reports · 2022Review
- TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome.ISME communications · 2022Article
- Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research.Toxicological sciences : an official journal of the Society of Toxicology · 2022Review
- MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data.Briefings in bioinformatics · 2022Article
- Response and resilience of anammox consortia to nutrient starvation.Microbiome · 2022Article
- Dysbiotic microbes and how to find them: a review of microbiome profiling in prostate cancer.Journal of experimental & clinical cancer research : CR · 2022Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples. Compared to an existing web application server, MetaTrans shows more efficiency in terms of runtime (around 2 hours per million of transcripts) and presents adapted tools to compare gene expression levels. It has been tested with a human gut microbiome database but also proposes an option to use a general database in order to analyze other ecosystems. For the installation and use of the pipeline, we provide a detailed guide at the following website (www.metatrans.org).
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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.