This repository contains files and scripts needed to run pathogen analysis using amplicon sequences and QIIME (OTU table, scripts and mapping file).
In order to run the scripts in this repository, you will need to have the following installed:
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QIIME 1.9.1
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Standalone NCBI-blast 2.7.1+
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NCBI formatted database (e.g NCBI's 16S or 18S database)
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R v3.4 and above
Please read the file 'how_to_run_pathogenAnalysis.txt' for instructions on how to run the analysis.
If you find any of the scripts or files in this repository useful, please cite:
Obayomi, O., Bernstein, N., Edelstein, M., Vonshak, A., Ghazayarn, L., Ben-Hur, M., Tebbe, C.C., Gillor, O., 2019. Importance of soil texture to the fate of pathogens introduced by irrigation with treated wastewater. Sci. Total Environ. 653, 886–896. https://doi.org/10.1016/j.scitotenv.2018.10.378