The mustache workflow is designed to identify insertion events from paired-end metagenomic sequencing data. The required inputs are FASTQ files, reference genomes for bacterial species of interest, reference sequences for insertion sequences of interst, and read-level taxonomic classifications for both forward and reverse reads. The approach if this workflow enables scientists to identify longitudinal changes in strain-level insertion event frequency, as well as variations between individuals and body sites.

Mustache is implemented as a snakemake workflow. Snakemake is a workflow management system that allows for all the tasks to be easily parallelized. I strongly recommend you read about snakemake and even complete the beginner's tutorial here.

This pipeline requires you to create a conda environment, so that you can then easily download all of the required packages and run the workflow on any system you'd like. If you haven't already, download anaconda here. I strongly suggest you learn the basics of anaconda before continuing with installation.

From a unix terminal, type the following:

git clone https://github.com/durrantmm/mustache.git
cd mustache

You are now in the downloaded mustache directory.

Let's now create a conda environment from the provided environment.yaml file in the mustache directory:

conda env create -f environment.yaml

You can then activate the mustache conda environment with the command:

source activate mustache

Mustache should now be ready to go, but first let's test the installation. From the mustache directory, run

snakemake --config output_dir=test -p

After a few seconds of running, you should see the process end with the message

MUSTACHE FINISHED WITH NO EXCEPTIONS!

Mustache should now be properly installed.