noahaus/metri

Multiomic integration of metagenomic and metatranscriptomic data

For microbial communities of interest, the ability to understand the community structure while simultaneously characterizing relevant biomarkers associated with their presence can provide great insights to the biological activies happening in these systems. Integrative analyses of these systems through multi-omics is an up-and-coming approach to study microbial systems to a greater extent. Techniques that output metagenomic and metatranscriptomic data, and their subsequent joint analysis, should provide rapid insights about potential key players and biomarkers in a microbial community, but widely accessible and open-source tools are limited to achieve this level of integration. In the proposed project, I will construct METRI, a Nextflow and Conda developed multi-omic framework for the joint integration of next generation sequencing microbiome DNA and RNA data. Inital testing of the pipeline was conducted by analyzing publically available data from the Inflammatory Bowel Disease Multiomics Database and also from the microbiomes of naturally decomposing deadwoods (Tláskal et al., 2021). This tool will be designed as a general framework to investigate key microbial species-level events in a microbial systems related to experimental differences.

metri's Issues

Metatranscriptomic Workflow

Merging of two workflows

MAG workflow