Resources

The Our Wastewater Footprint website is a living resource with data and resources concerning human wastewater effects on water quality in the northern Gulf of Mexico. 

Our Wastewater Footprint includes the Alabama MST Metadata Clearinghouse, which contains microbial source-tracking and other monitoring metadata compiled from various monitoring organizations and research groups. Data can be contributed to the Alabama MST Clearinghouse via the Questionnare on that site.

Selected review papers on microbial source tracking and eDNA metagenomics:

Aplakidou, E., et al. (2024). Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational and Structural Biotechnology Journal, 23: pp. 2011-2033 DOI: 10.1016/j.csbj.2024.04.060

Garlapati, D., et al. (2019). A review on the applications and recent advances in environmental DNA (eDNA) metagenomics. Rev Environ Sci Biotechnol 18, 389–411 https://doi.org/10.1007/s11157-019-09501-4

Raza, S., et al. (2021). Microbial source tracking using metagenomics and other new technologies. J Microbiol. 59, 259–269 https://doi.org/10.1007/s12275-021-0668-9

Selected bioinformatics resource pages:

Anvi’o is a free computational platform that integrates microbial bioinformatic programs through easy-to-use workflows and interactive visualizations. There is extensive documentation, workflows, and help available for Anvi’o programs on the Anvi’o website, github, and discord.

This Metagenomic Protocol contains details on the components of the Anvi’o metagenomics workflow.

The Tinybio intern tutorials site (https://docs.tinybio.cloud/docs/) contains software guides and tutorials for a variety of bioinformatic tasks.