/workflow_metagenomic_environmental_surveillance

Primary LanguageRMIT LicenseMIT

An improved workflow for accurate and robust environmental surveillance using metagenomics

For help or any data requests, please contact Jiaxian Shen at jiaxianshen2022@u.northwestern.edu

In order to run the analyses yourself, please do the following:

  • Download the data and script from the folder. The raw shotgun metagenomic sequencing data are available in the NCBI SRA repository under Bioproject number PRJNA765404.

  • Unzip the data

  • Change the working directory to the folder containing the downloaded data.

  • Run the analyses.

R scripts were run under version v4.0.4. Bash scripts were run on Northwestern Quest High Performance Computing Cluster.

Feel free to contact me if you encounter issues or need clarifications.