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Learning outcomes

After having completed this chapter you will be able to:

  • Develop a basic pipeline for alignment-based analysis of a long-read sequencing dataset
  • Answer biological questions based on the analysis resulting from the pipeline


The last part of this course will consist of project-based-learning. This means that you will work in groups on a single question. We will split up into groups of five people.

If working independently

If you are working independently, you probably can not work in a group. However, you can test your skills with these real biological datasets. Realize that the datasets and calculations are (much) bigger compared to the exercises, so check if your computer is up for it. You’ll probably need around 4 cores, 16G of RAM and 10G of harddisk.

If online

If the course takes place online, we will use break-out rooms to communicate within groups. Please stay in the break-out room during the day, also if you are working individually.

Roles & organisation

Project based learning is about learning by doing, but also about peer instruction. This means that you will be both a learner and a teacher. There will be differences in levels among participants, but because of that, some will learn efficiently from people that have just learned, and others will teach and increase their understanding.

Each project has tasks and questions. By performing the tasks, you should be able to answer the questions. At the start of the project, make sure that each of you gets a task assigned. You should consider the tasks and questions as a guidance. If interesting questions pop up during the project, you are encouraged to work on those. Also, you don’t have to perform all the tasks and answer all the questions.

In the afternoon of day 1, you will divide the initial tasks, and start on the project. On day 2, you can work on the project in the morning and in the first part of the afternoon. We will conclude the projects with a 10-minute presentation of each group.

Working directories

Each group has access to a shared working directory. It is mounted in the root directory (/). Make a soft link in your home directory:

cd ~
ln -s /group_work/<group name> ./

Now you can find your group directory at ~/<group name>. Use this as much as possible.


Do not remove the soft link with rm -r, this will delete the entire source directory. If you want to remove only the softlink, use rm (without -r), or unlink. More info here.