MetaTrans: an open-source pipeline for metatranscriptomics.

Area of Science:

• Microbiology
• Bioinformatics
• Computational Biology

Background:

• High-throughput sequencing generates vast data, challenging computational resources for meta-omics.
• Analyzing microbial community structure and function requires efficient bioinformatic pipelines.

Purpose of the Study:

• To introduce MetaTrans, an efficient open-source pipeline for analyzing microbial community RNA-Seq data.
• To enable taxonomic and gene expression analysis of active microbial communities.

Main Methods:

• MetaTrans is a multi-threaded pipeline for RNA-Seq analysis.
• It includes quality control, rRNA removal, read mapping to functional databases, and differential gene expression analysis.
• The pipeline was validated using synthetic communities, prior study data, and human fecal samples.

Main Results:

• MetaTrans demonstrates high efficiency, with a runtime of approximately 2 hours per million transcripts.
• It offers adapted tools for comparing gene expression levels, surpassing existing web application servers.
• The pipeline is adaptable for human gut microbiome and general ecosystem analyses.

Conclusions:

• MetaTrans provides an efficient and versatile solution for microbial community RNA-Seq analysis.
• Its performance and features facilitate deeper understanding of microbial community dynamics.
• The open-source pipeline is accessible with a detailed guide available online.