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metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.

Limuxuan He1, Quan Zou1,2, Yansu Wang3

  • 1Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China.

BMC Bioinformatics
|April 26, 2025
PubMed
Summary
This summary is machine-generated.

We developed metaTP, a bioinformatics pipeline for analyzing meta-transcriptomic data. This tool enhances reproducibility and interpretation of microbiome RNA sequencing data for microbial ecology research.

Keywords:
Co-expression network analysisFunctional annotationMeta-transcriptomeTranscript expression quantificationmetaTP pipeline

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Area of Science:

  • Microbial Ecology
  • Bioinformatics
  • Transcriptomics

Background:

  • Sequencing technologies enable meta-transcriptomic studies for microbial ecology.
  • Omics data analysis requires multiple bioinformatics tools.
  • Variations in processing methods compromise reproducibility in microbiome research.

Purpose of the Study:

  • To develop an efficient analytical workflow for meta-transcriptomic data.
  • To ensure repeatability, reproducibility, and traceability of microbiome research results.
  • To improve accessibility and interpretation of microbiota RNA-Seq data.

Main Methods:

  • Developed metaTP, a pipeline integrating bioinformatics tools.
  • Included quality control, non-coding RNA removal, and transcript expression quantification.
  • Utilized reference indexes from protein-coding sequences for quantification.
  • Incorporated differential gene expression, functional annotation, and co-expression network analysis.

Main Results:

  • metaTP comprehensively analyzes meta-transcriptomic data.
  • Quantification relies on reference indexes, overcoming database limitations.
  • Pipeline includes co-expression network analysis with topological property calculation.
  • Facilitates intuitive explanations for correlated gene sets.

Conclusions:

  • Created a conda package for metaTP, ensuring flexibility and versatility.
  • The metaTP pipeline is freely available for meta-transcriptomic data analysis.
  • metaTP supports researchers in microbiota-related biological inquiries.