SAS Bioinformatics Data Pre-Processing and Analysis, Hochschule für Life Sciences FHNW

You will learn how to work with raw NGS and nanopore sequencing data and apply key bioinformatics workflows, including quality control, read alignment, variant calling and metagenomics analysis. You will gain practical experience with file formats such as FASTQ, BAM and VCF, and use tools like the Genome Analysis Toolkit (GATK) to analyze genomic data and solve real-world sequencing problems.

After completing the SAS, you will be able to:

• Process and manage raw sequencing data using standard bioinformatics file formats (FASTQ, BAM, VCF).
• Apply quality control methods to assess sequencing data quality and improve downstream analysis reliability.
• Perform read alignment and variant calling using established computational workflows.
• Use the Genome Analysis Toolkit (GATK) to analyze genomic variation in sequencing datasets.
• Design and apply metagenomics and sequencing data pipelines to solve bioinformatics problems.

This SAS is for you if you work in life sciences, healthcare or research and want to build practical skills in bioinformatics. It is particularly relevant if you:

• Work with or plan to work with next-generation and nanopore sequencing data
• Work in biotech, pharma or a related industry where sequencing analysis is becoming essential

You should have a basic understanding of molecular biology, some hands-on experience with a programming language such as Python, and strong motivation to strengthen your computational skills.

This SAS is the second of three modules within the CAS Applied Bioinformatics: Next- and 3rd Generation Sequencing Data Analysis. It is offered online over four days. This module introduces core techniques for handling raw sequencing data, including relevant file formats, quality control, read alignment, variant calling and metagenomics analysis.

• File formats: FASTQ, BAM, VCF
• Genome Analysis Toolkit (GATK)
• Quality control procedures
• Read alignment techniques
• Variant calling workflows
• Metagenomics pipelines

This module builds a solid foundation required for biological and clinical interpretation of sequencing data covered later in the programme. At the end of the module, a multiple-choice questionnaire (pass/fail) is available, if you would like to receive ECTS credits. The module can be allocated to the CAS Applied Bioinformatics: Next- and 3rd Generation Sequencing Data Analysis within three years. If you have successfully completed all SAS of this CAS programme and wish to receive the Certificate of Advanced Studies (CAS), please contact us for the final written assignment.

• Prof. Dr. Abdullah Kahraman, Programme Manager
• Dr. Thomas Wieland, Sr. Director Strategic Operations, Foundation Medicine
• Dr. Aashil Batavia, Sr. Expert Data Scientist, Novartis

The following programme admission requirements apply:

• Tertiary A: Higher education qualification (at least a Bachelor’s degree) and at least 2 years’ practical experience relevant to the programme,
• Tertiary B: Colleges of Higher Education Diploma (HF), Advanced Federal Diploma of Higher Education (HFP) or Federal Diploma Higher Education (BP), and at least 5 years’ practical experience relevant to the programme,
• Individuals without a Tertiary A or B qualification may be admitted if they cumulatively meet the following admission criteria:
• at least 10 years’ professional experience in a field relevant to the programme, of which at least 5 years in a managerial or senior specialist role
• additional qualifications (various non-formal, extensive further training courses or partial completion (>50%) of a tertiary qualification)
• evidence of knowledge of academic work or a willingness to acquire this in advance.

As the instruction and educational materials are in English, proficiency in English (minimum level C1) is a prerequisite.

A personal notebook/laptop is required for the programme.