Amsterdam Science Park Study Group

In this workshop, you will learn how to carry out a common metagenomics workflow – identifying Operational Taxonomic Unities (OTUs) among samples taken from two metagenomes within a location. We will be starting with a set of sequenced reads (.fastq files), performing some quality control steps, assembly those reads into contigs, and ending by identifying and visualizing the OTUs among these samples.

The microbial diversity will be further analysed using R enabling you to generate publication-grade figures and fully explore the outcomes of a metagenomics experiment.

As you progress through this lesson, keep in mind that, even if you aren’t going to be doing this same workflow in your research, you will be learning some very important lessons about using command-line bioinformatics tools as well as downstream analysis in R. What you learn here will enable you to use a variety of bioinformatics tools with confidence and greatly enhance your research efficiency and productivity.

People involved: Marc Galland (UvA, organiser), Jesse Kerkvliet (Utrecht UMC, instructor), Misha Paauw (UvA, SILS, instructor), .

Workshop website: https://scienceparkstudygroup.github.io/2022-12-08-shotgun-metagenomics-workshop/

How to register: to be announced.

Data visualization is the transformation of data into pictures. This transformation is done to better understand and communicate the data, in terms of relationships, distributions and other aspects. Data visualization is important at various stages of experimental research, i.e. for the exploration, interpretation and publication of data. But how do you visualize data, practically, and efficiently?

R is a popular open source software package with great support for data visualization. This workshop aims to get you started with data visualization in R. This will be done in base R as well as with the {ggplot2} package. After an introduction, several data visualizations will be demonstrated in a hands-on session.

Call for input

We would love to hear from you! Which type of data visualization are you interested in? Do you have a visualization challenge and/or would like us to use your data for the hands-on session? Have you seen a data visualization that you want to learn to reproduce? Send your data and ideas to Anna Heintz-Buschart  or Joachim Goedhart.

To prepare the workshop, we would like to have your response before July 31st.

Prerequisites: This workshop uses R/Rstudio. You can follow the workshop with or without prior experience with R.