Setup

Before we dive into the tutorial, let’s make sure we have all the necessary components in place. Make sure you have a working MOSHPIT environment available - please follow the instructions from the developer QIIME 2 documentation to install all the required components. These installation instructions will also become available through the official QIIME 2 user documentation in the 2025.4 release later this year.

In this tutorial we will be storing all the data in the QIIME 2 cache. To learn more about how the cache works, you can refer to the Using an Artifact Cache tutorial. (Note that all calls to qiime in that document can be replaced by calls to mosh.) You should create a single cache directory in the current working directory by running the following command:

mosh tools cache-create --cache ./cache

Note on parallelization

While we do not explicitly mention parallelization in the tutorial, many of the QIIME 2 actions can be parallelized by executing actions on smaller subsets of the data called partitions. To make use of parallelization, you will need a parsl config file which will define the resources available to the parallel execution. Here is an example of a config file which was used to assemble contigs through the assemble-megahit action:

[parsl]

[[parsl.executors]]
class = "HighThroughputExecutor"
label = "default"
max_workers = 1

[parsl.executors.provider]
class = "SlurmProvider"
scheduler_options = "#SBATCH --mem-per-cpu=4G"
exclusive = false
worker_init = "source ~/.bashrc && conda activate q2-metagenome-2024.5"
walltime = "24:00:00"
nodes_per_block = 1
cores_per_node = 24
max_blocks = 14

To learn more about how to configure parallelization in QIIME 2, please consult the official documentation.

Note

To examine your generated QIIME 2 visualizations, you can use QIIME 2 View.