Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments

This project represents the first chapter of my PhD, in which I compare metagenomics and total RNA-Seq data-processing pipelines to identify which sequencing method and pipeline give the most accurate estimate of the diversity of a microbial mock community. The repo contains scripts to run all pipelines and statistics.

The project is part of the following publication:
Hempel C. A., Wright N., Harvie J., Hleap J. S., Adamowicz S. J., and Steinke D. (2022): Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments. Nucleic Acids Research 50(16):9279–9293. https://doi.org/10.1093/nar/gkac689

The processed pipelines are combinations of typically utilized data-processing tools, and the following figure gives an overview of the tested tools per processing step. We tested all combinations of tools (1,536 combinations in total).

The workflow from sample preparation to accuracy evaluation is shown in the following: