Arbuscular mycorrhizal fungi composition in soils of switchgrass harvested for bioenergy under alternate nitrogen management

Detailed below is the reproducible workflow for the data analysis performed in Dirks & Jackson (2020). All the commands should be executed from the project root directory.

1: Import GitHub Project

Open Terminal and change the current working directory to the location where you want this project to be cloned. Clone the repository with git clone and enter the new directory.

git clone https://github.com/aldendirks/amf_metabarcoding.git
cd ./amf_metabarcoding

2: Acquire Raw Sequence Data

From the project root directory, run the get_sra.sh script to install SRA Toolkit and download the raw sequence data in fastq format from NCBI SRA BioProject accession PRJNA590305. You will be prompted to specify a download/cache area for downloaded files. Set the workspace directory to ./data/seqs/bioinfo/04_fastq by navigating to Cache, pressing o on the keyboard to select a directory, and using the arrow keys and enter to navigate to the correct location.

bash scripts/get_sra.sh

3: Bioinformatics

3a: Process CCS into ASVs with DADA2

Open the scripts/dada.R script in R and execute the commands sequentially to process the fastq circular consensus sequences into ASVs with DADA2.