This is a two-day course that demonstrates a typical workflow for microbial marker gene (16S, 18S, and ITS) sequencing analysis, from raw FASTQ files to a wide range of plots, tables, and statistics. The course aims to teach attendees how to use the most appropriate tools for their analysis, and write their own pipeline for marker gene analysis. The primary goal of this course is not only to equip attendees with the coding skills required for their analysis, but to explain the principles behind the tools and methods.

Day one of the course is centred around using the QIIME2 package to generate sequence variants, taxonomic data, some alpha and beta diversity statistics, and functional inference via PICRUSt2. Attendees will learn about how QIIME2 works and why it is useful, as well as breaking down each individual step to see what is happening to their data and how exactly their results are generated.

Day two takes many of the outputs from QIIME2 and uses them in R to generate more bespoke plots, figures, and statistics, and employ a wide range of statistical tools such as differential abundance and supervised learning methods. This day is geared towards interrogating all the data generated on the first day, to ask specific biological questions of the data, and to generate high-level statistical results in R.

This course has been carefully designed to accommodate a range of competency levels, but is generally aimed at those with little-to-no previous bioinformatics or command line experience.

To register your interest, please fill in the registration form. Note that you should have completed our course 'Introduction to Practical Bioinformatics' before attending this course