NGS - Quality Control, Alignment, Visualisation

27 February - 01 March 2019
Cancellation deadline:
13 February 2019
Walid Gharib
Omics data analysis
0.75 credits

This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available.


Usage of NGS is increasing in several biological fields due to a very rapid decrease in cost. However, it often results in hundreds of Gbs of data making the downstream analysis very challenging and requires bioinformatics skills.

In this module, we will introduce the most used sequencing technologies and explain their decryption concepts.

We will also introduce the repositories e.g. the European Nucleotide Archive (ENA), Sequence Read Archive (SRA) from which you could retrieve raw data based on specific experiments. We will practice the usage of command line tools to search and fetch NGS raw data in a powerful way.

Finally, using different datasets, we will practice screening for quality control, filtering reads for better downstream analysis, mapping reads to reference genome and visualize the output.


This course is intended for life scientists who are already dealing with NGS data or willing to efficiently use publicly available NGS data, and would like to be able to start analysing them.

Learning objectives

At the end of the course participants should be able to:

  • distinguish between the different NGS technologies
  • navigate and retrieve efficiently datasets from the The European Nucleotide Archive (ENA) and the Sequence Read Archive (SRA)
  • perform quality control for better downstream analysis, mapping reads to reference genome and visualizing the output.


Knowledge / competencies:

Participants should have a basic understanding of working with command line tools on Linux or Windows-based operating systems. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module.


Participants should bring their own computers and chargers. Computers should have at least 4 GB RAM, 50 GB free disk space, and WIFI preinstalled.

Participants should install "The Integrative Genome Viewer (IGV)" on their respective machines.


This course is over subscribed. You can still add your name to the waiting list by applying using the button at the bottom of this page. You will only be contacted if a place becomes available.

The registration fees for academics are 180 CHF and 900 CHF for for-profit companies.

This includes course content material and coffee breaks. You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Deadline for registration and free-of-charge cancellation is set to February 13. Cancellation after this date will not be reimbursed.

Please note that participation to SIB courses is subject to this and other general conditions, available here.

Location & Time

Universität Bern, Hochschulstrasse 4 (main building of the University of Bern), classroom 331, 3. OG West

The course will start at 9:00 and end around 17:00. Precise information will be provided to the participants on due time.


Wednesday 27 February

Introduction to technologies and applications, NCBI E-Utilities and sequencing data retrieval  

9:15 - 10:30 - Introduction to technologies and applications (1)

  • Ion Torrent Sequencing - Semiconductor sequencing
  • llumina - sequencing by synthesis

10:30 - 11:00 - Coffee Break

11:30 - 12:15 - Introduction to technologies and applications (2)

  • Pacific Biosciences - SMRT Sequencing
  • Oxford Nanopores - MinIon, GridIon

12:15 - 13:30 - Lunch Break

13:30 - 13:45 - NCBI: E-utilities using Unix command line
13:45 - 15:00 - E-utilities usage - Practicals

15:00 - 15:30 - Coffee break

15:30 - 15:45 - Sequencing archives, SRA, ENA and DDBJ
15h45 - 17:00 - Fetching sequencing data - Practicals (Combining E-utilities and SRA tools)

Thursday 28 February

File Formats, quality assessment, cutting/trimming/filtering and sequence alignement

9:00 - 10:00: File formats and Quality controls
9:45 - 10:30: Interpretation of a Fastqc report and acting upon for cutting/trimming reads

10:30 - 11:00: Coffee break

11:00 - 12:15: Quality control - Practicals

                        - Trimming/filtering quality control - Practicals

12:15 - 13:30 - Lunch Break

13:30 - 15:30 -  Alignment to a reference genome - Small intro and practicals
15h30 - 17:00 -  Sorting, Indexing the alignment and quick visualization using IGV genome viewer

Friday 29 February

9:00 - 10:30: Visualisation using IGV lecture 
10:30 - 11:00: Coffee break

11:00 - 12:15:  Practicals using cancer variants dataset

12:15 - 13:30: Lunch Break

13:30 - 15:30: Practicals using RNAseq and CHIPseq datasets

15h30 - 17:00: useful tips and tricks in NGS/concluding remarks


Additional information

The course will be taught by Walid Gharib.

Coordination: Patricia Palagi, Training group at SIB

We will recommend 0.75 ECTS credits for this course (given a passed exam (optional) at the end of the session). 

You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact