Qiime2

Overview

Quantitative Insights Into Microbial Ecology (QIIME) is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication-quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.

QIIME Features:

Automatically track your analyses with decentralized data provenance — no more guesswork on what commands were run!
Interactively explore your data with beautiful visualizations that provide new perspectives.
Easily share results with your team, even those members without QIIME 2 installed.
Plugin-based system — your favorite microbiome methods all in one place.

Notes:

ARCC currently does not monitor the current/latest versions of the software. If you require an update to a version please remember to put a request in and include any plugins you require.

Qiime2 does have a collection of plugins. The ones available can be seen by typing qiime from the command line once the module has been loaded, as shown below. If you require a plugin not listed please put a request into ARCC and we can explore how best to make this available.
We are still learning to what extent qiime2 is parallelized. At this moment we believe that it can only run on a single node. Some plugins can make use of multiple cores on that node, which can be found by reading the documentation relating to that plugin. Since there is no consistent syntax across the plugins on how to make use of this, if you can not work it out yourself please contact ARCC and we'll be happy to help.
If the usage of the software increases and the demand warrants the managing of the central reference database then ARCC is happy to discuss and explore.

Note on Plugins and Versions

You will notice that the available plugins are not all available in every qiime2 version. Plugins are open source, and developed by third-parties and thus not necessarily regularly updated when Qiime2 is updated. ARCC will try and see if a plugin will install when we update Qiime2, but in a lot of cases we are running into dependency issues where a plugin has been developed using older versions of libraries than that used by the latest Qiime version. Until the plugin developer releases a new version compatible with the latest version of Qiime there is nothing we can do.

Using

Use the module name qiime2 to discover versions available and to load the application.

Multicore

Out of the box, qiime2 does not automatically run in parallel, but some of the plugins/commands can be configured to use multiple cores.
One example is classify-sklearn which is a pre-fitted sklearn-based taxonomy classifier. This command has the --p-n-jobs option that allows multiple cores to be used.

Getting Help

There are a number of commands to get help from the command-line:

[@blog1 ~]$ module load qiime2/2023.5
[@blog1 ~]$ qiime
Usage: qiime [OPTIONS] COMMAND [ARGS]...

  QIIME 2 command-line interface (q2cli)
  --------------------------------------

  To get help with QIIME 2, visit https://qiime2.org.

  To enable tab completion in Bash, run the following command or add it to
  your .bashrc/.bash_profile:

      source tab-qiime

  To enable tab completion in ZSH, run the following commands or add them to
  your .zshrc:

      autoload -Uz compinit && compinit
      autoload bashcompinit && bashcompinit
      source tab-qiime

Options:
  --version   Show the version and exit.
  --help      Show this message and exit.

Commands:
  info                Display information about current deployment.
  tools               Tools for working with QIIME 2 files.
  dev                 Utilities for developers and advanced users.
  alignment           Plugin for generating and manipulating alignments.
  composition         Plugin for compositional data analysis.
  cutadapt            Plugin for removing adapter sequences, primers, and
                      other unwanted sequence from sequence data.
  dada2               Plugin for sequence quality control with DADA2.
  deblur              Plugin for sequence quality control with Deblur.
  demux               Plugin for demultiplexing & viewing sequence quality.
  diversity           Plugin for exploring community diversity.
  diversity-lib       Plugin for computing community diversity.
  emperor             Plugin for ordination plotting with Emperor.
  feature-classifier  Plugin for taxonomic classification.
  feature-table       Plugin for working with sample by feature tables.
  fragment-insertion  Plugin for extending phylogenies.
  gneiss              Plugin for building compositional models.