Here you can find the course material for the SIB course ‘NGS - Quality control, Alignment, Visualisation’. You can follow this course enrolled (check out upcoming training courses) or in your own time.
After this course, you will be able to:
- Understand the basics of the different NGS technologies
- Perform quality control for better downstream analysis
- Align reads to a reference genome
- Visualize the output
Teachers
Authors
Course schedule
Day 1
| block | start | end | subject |
|---|---|---|---|
| introduction | 9:00 AM | 9:30 AM | Introduction |
| block 1 | 9:30 AM | 10:30 AM | Sequencing technologies |
| 10:30 AM | 11:00 AM | BREAK | |
| block 2 | 11:00 AM | 12:30 PM | Setup + Reproducibility |
| 12:30 PM | 1:30 PM | BREAK | |
| block 3 | 1:30 PM | 3:00 PM | Quality control |
| 3:00 PM | 3:30 PM | BREAK | |
| block 4 | 3:30 PM | 5:15 PM | Group work |
Day 2
| block | start | end | subject |
|---|---|---|---|
| block 1 | 9:00 AM | 10:30 AM | Read alignment |
| 10:30 AM | 11:00 AM | BREAK | |
| block 2 | 11:00 AM | 12:30 PM | File types |
| 12:30 PM | 1:30 PM | BREAK | |
| block 3 | 1:30 PM | 3:00 PM | Samtools |
| 3:00 PM | 3:30 PM | BREAK | |
| block 4 | 3:30 PM | 5:15 PM | Group work |
Day 3
| block | start | end | subject |
|---|---|---|---|
| block 1 | 9:00 AM | 10:30 PM | IGV and visualisation |
| 10:30 AM | 11:00 AM | BREAK | |
| block 2 | 11:00 AM | 12:30 PM | Group work |
| 12:30 PM | 1:30 PM | BREAK | |
| block 3 | 1:30 PM | 3:00 PM | Group work |
| 3:00 PM | 3:30 PM | BREAK | |
| block 4 | 3:30 PM | 5:15 PM | Presentations |
License & copyright
License: CC BY-SA 4.0
Copyright: SIB Swiss Institute of Bioinformatics
Material
- This website
- Zoom meeting (through mail)
- Google doc (through mail)
- Slack channel
Learning outcomes
After this course, you will be able to:
- Understand the basics of the different NGS technologies
- Perform quality control for better downstream analysis
- Align reads to a reference genome
- Visualise the output
Learning experiences
This course will consist of lectures, exercises and polls. During exercises, you are free to discuss with other participants. During lectures, focus on the lecture only.
Exercises
Each block has practical work involved. Some more than others. The practicals are subdivided into chapters, and we’ll have a (short) discussion after each chapter. All answers to the practicals are incorporated, but they are hidden. Do the exercise first by yourself, before checking out the answer. If your answer is different from the answer in the practicals, try to figure out why they are different.
Asking questions
During lectures, you are encouraged to raise your hand if you have questions (if in-person), or use the Zoom functionality (if online). Use the ‘Reactions’ button:
A main source of communication will be our slack channel. Ask background questions that interest you personally at #background. During the exercises, e.g. if you are stuck or don’t understand what is going on, use the slack channel #q-and-a. This channel is not only meant for asking questions but also for answering questions of other participants. If you are replying to a question, use the “reply in thread” option:
The teacher will review the answers, and add/modify if necessary. If you’re really stuck and need specific tutor support, write the teachers or helpers personally.
To summarise:
- During lectures: raise hand/zoom functionality
- Personal interest questions: #background
- During exercises: #q-and-a on slack
You can do this course completely independently without a teacher. To do the exercises, we will set things up locally with a Docker container. If there any issues, use the issues page on our github repository.
Note
It might take us a while to respond to issues. Therefore, first check if a similar issue already exists, and/or try to fix it yourself. There’s a lot of documentation/fora/threads on the web!
Learning outcomes
After this course, you will be able to:
- Understand the basics of the different NGS technologies
- Perform quality control for better downstream analysis
- Align reads to a reference genome
- Visualize the output
Exercises
Each block has practical work involved. Some more than others. All answers to the practicals are incorporated, but they are hidden. Do the exercise first by yourself, before checking out the answer. If your answer is different from the answer in the practicals, try to figure out why they are different.