Getting started

The data package

You can download the data package used in this workshop from Zenodo, Please select versie 2021.06.2. This data package contains the following:

  • Raw sequencing data with quality scores as demultiplexed fastq.gz files.

  • The SILVA 16S taxonomic database version 138.

  • The taxonomic classifier, specifically pre-trained to use on this data set.

  • All intermediate results, such that you can choose to skip very time consuming steps.

Windows subsystem for Linux - users

In order to access the data package from within your Linux file system, copy your data package to your Linux home​. Where is your Linux home? In your Terminal, enter the following to view the current directory in Windows File Explorer​

cd ~
explorer.exe . ## don't forget the dot

How to use this tutorial?

Where to start

Assuming the data package archive (metabarcoding-qiime2-datapackage-v2021.06.2.tar.gz) is in your home directory, extract it and navigate into the metabarcoding-qiime2-datapackage-v2021.06.2 directory, like so:

cd ~
tar -xzvf metabarcoding-qiime2-datapackage-v2021.06.2.tar.gz
cd metabarcoding-qiime2-datapackage-v2021.06.2
ls

The last command shows you which files and subdirectories are in your current directory. If it looks like this you are golden:

dada2  data  db  deblur  exports  logs  prep  README.txt  taxonomy  WALKTHROUGH.sh

Important

For the remainder of the tutorial, make sure you always run the commands from the metabarcoding-qiime2-datapackage-v2021.06.2 directory, otherwise you will get a No such file or directory error.

Activating your conda environment

If you installed QIIME2 following the instruction in the General Information, all QIIME2 tools are inside a dedicated conda environment called qiime2-2021.2. As long as you are outside this environment, you will not be able to use the QIIME2 commands. Before starting a session, make sure to activate the qiime2-2021.2 environment. You will know whether you are in the correct environment if your prompt starts with (qiime2-2021.2).

Important

Before starting your analyses activate your conda environment: conda activate qiime2-2021.2

Skipping steps

It is not necessary for this workshop to have a very powerful computer. You can run most of the analyses on a laptop, and if that does not work, you can skip that step and continue with the intermediate files in your data package.

Tip

When you follow the steps in this tutorial, you will overwrite the pre-computed intermediate files present in your data package. Make sure to keep a copy of the original data package, such that you can always restore these pre-computed files when needed.