Reconstruction of Small Subunit Ribosomal RNA from High-Throughput Sequencing Data: A Comparative Study of Metagenomics and Total RNA Sequencing
This project represents the second chapter of my PhD, in which I compare metagenomics and total RNA-Seq in terms of their Small Subunit (SSU) ribosomal RNA (rRNA) reconstruction completeness and further test the impact of data-processing tools on completeness. The evaluation is based on a microbial mock community as well as aquarium samples. The repo contains scripts to run data-processing pipelines, to determine completeness, and for statistical analysis.
The project is part of the following publication:
Hempel C. A., Carson S. E. E., Elliott T. A., Adamowicz S. J., and Steinke D. (2023). Reconstruction of small subunit ribosomal RNA from high-throughput sequencing data: A comparative study of metagenomics and total RNA sequencing. Methods in Ecology and Evolution, 00, 1–16. https://doi.org/10.1111/2041-210X.14149
The entire workflow is shown in the following:
