Code for data processing, analysis, and visualization of whole shotgun metagenomic data for milkweed phyllospheres and rhizospheres. All code for these steps are in the Bash_code, Functional_profiling, PSM_detoxification_profiling, and Taxonomic_profiling directories.
Bash_code contains all the batch scripts needed to process the next-generation sequencing data used in this project. From paired read quality control and demultiplexing, to metagenome assembly gene prediction and annotation. The data produced during these steps are used for further analysis and visualization.
Functional_profiling contains all the R scripts used for analysis and visualization of the metagenome assembly functional profiling.
PSM_detoxification_profiling PSM_detoxification_profiling contains all the R scripts used for analysis and visualization of potential plant secondary metabolite metabolism genes in the milkweed phyllospheres and rhizospheres. This was conducted on the same metagenome assembly used in the functional profiling analysis.
Taxonomic_profiling contains all the R scripts used for analysis and visualization of the taxonomic profiling for the microbial communities associated with the milkweed phyllospheres and rhizospheres.
This repository contains all the code necessary to replicate the data processing, analysis, and figure generation for the manuscript "Functional profiles of phyllosphere and rhizosphere metagenomes differ across milkweed species" authors: Thorsten Einar Hansen and Laramy Enders {UPDATE w/ REFERENCE & LINK when published}. To replicate this analysis, first download raw sequence data from NCBI's SRA database, BioProject number PRJNA1121629.
If you have any questions concerning the data, analysis, or manuscript please contact me at thorstenhansen92@gmail.com.