Qiime2

This is an introduction to data analysis with metabarcoding data. We will primarily use the Qiime2 software package, but we don’t want to present that as the only way to go. We will a encourage a flexible approach, so, we will go over how to import into Qiime2 and likewise export the results so they can be used by other programs. We will cover the basic elements of virtually all metabarcoding analytic approaches, as a starting point.

The Qiime2 multiverse is itself a tool to utilise multiple other programs, and there are many options. When you install Qiime, the other software is also installed, so you can run them through Qiime or on their own (as long as you are in the Qiime environment).

The main Qiime2 webpage has many good tutorials, instructions, and descriptions of the relevant concepts and theory. The pages here are not meant as a replacement for that wealth of information, but rather provide an initial starting point, accompanied by in-class instruction. This workshop will follow through some standard workflows, with other examples given and referencing Qiime2 web materials for further information.

Lessons

• Basic Tools for this Workshop

• Overview of Qiime2

• Getting Started

• Clustering

• Diversity Analyses

• Taxonomy Assignment

• Taxonomy Databases

• Creating A Taxonomy Database

• Importing and Graphing in R

Important Links

Qiime2docs Main index of all Qiime2 content

Qiime2view A web browser tool for viewing Qiime2 visualisations

Extended Lessons

• More on importing data

• Filtering Tables