Full workflow for collaborators

As of June 29, 2020, the full ITS workflow should (pending any bugs) consists of the following scripts in the ./code/workflow directory, run in order:

00_new_server_setup.R

01a_dada2_workflow_its.R

02a_dada2_to_phyloseq_its.R

Parameters should be configured to suit your file system structure by making direct edits to params.R.

Ensure that you have installed all dependencies including R packages and additional software. Of particular note:

• You will need to install cutadapt to use 01a_dada2_worfklow_its.R. Installation instructions can be found here. (Note that if you have both Python2 and Python3 installed, you will need to replace pip with pip3 in the Quick Installation command.) Once installed, change the CUTADAPT_PATH variable in params.R to match the location of the cutadapt script on your system.
• Lastly, you will need to install the latest General FASTA Release of the UNITE database for taxonomy assignment of ITS sequences, available here. Once installed, change the UNITE_REF_PATH variable in params.R to match the location of the FASTA file on your system.

In addition, you should download the latest versions of R and RStudio before starting these scripts. You may also need to update Python to succesfully install cutadapt.

Be sure to run these with your working directory set to the project directory, not to the /code subdirectory.