Basic tools

We will start with the basic tools that you will need for this workshop.

Starting up Qiime2

Qiime2 is installed as a conda environment, so you will have to activate this to use it. Once you have logged in to the server, load the conda module and activate the environment:

module load conda

source activate qiime2-2019.7

In order to enable tab completion for Qiime commands:

source tab-qiime

This will need to be done each time you activate Qiime, or you can add it to your .bashrc or .bash_profile file

Basic Qiime2 commands

For getting help with any qiime command, you use –help

qiime --help

For this workshop, template commands will be provided initially. It is recommended that you copy these and paste them in a text editor, then change the input/output file names and any other parameters as needed. For the most part, the file names/variables that need to be changed will be in uppercase within curly brackets, like this:

qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-path {MANIFEST_FILE} \
  --output-path {QIIME_DEMUX}.qza \
  --input-format SingleEndFastqManifestPhred33V2

In the example above, you would change the name the {MANIFEST_FILE} and {QIIME_DEMUX} names. The suffixes .qza and .qzv always need to be used.

Viewing Qiime2 visuals

All visuals in Qiime2 are shown using a web browser. Because we are running this workshop on a server, you will need to download the visual files (any file ending in .qzv) to your laptop. Here is a quick primer on transferring files to/from the server.

To move a file to the server from your computer:

scp FILENAME username@boros.otago.ac.nz:qiime_workshop/

To move a file from the server to your computer, you switch the order. You have to provide a path to where on the computer you want the file.

scp username@boros.otago.ac.nz:FILENAME /PATH/TO/TARGET/FOLDER/

Let’s move the file example_viz.qzv from the qiime_workshop folder on boros. First we’ll create a directory on the Desktop for qiime files, then move into that directory to make it easier:

mkdir Desktop/qiime_files

cd Desktop/qiime_files

Now we can move the files from boros into the folder with just a .

scp username@boros.otago.ac.nz:qiime_workshop/example_viz.qzv .

If you have Qiime2 installed and running on your computer, you can view the visual files like this:

qiime tools view example_viz.qzv

Fortunately, you do not need to have Qiime2 installed to view the visuals. Go to this link:

Qiime2view

And you can open any visualisations on your computer. The website has some examples you can check out. Keep this website open as we proceed through the workshop.

There is yet another way to view Qiime2 visualisations. If you export any visual using qiime tools export it will convert the .qzv to a folder containing all the web code. You can then go into the folder, and double click on the index.html file, and it will open in a web browser will all the interactivity.

Qiime2 metadata file

For most downstream analyses in Qiime2, you need a metadata file. This is essentially a tab-delimited file that lists samples in the first column; additional columns can be used for other fields, and the state of each for each sample.

You can view the sample metadata for this data set here:

sample metadata FMT

Qiime2 provides a metadata tutorial to help prepare the metadata file, but you can start very simply with a list of samples.