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Instructor-led course

Provided by: Bioinformatics

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Introduction to genome variation analysis using NGS


This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

  • an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
  • an overview of available analytical tools and discussion of their limitations; and
  • hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here
  • Further details regarding eligibility criteria are available here
  • Basic experience of command line UNIX
  • Sufficient UNIX experience might be obtained from one of the many UNIX tutorials available online.
Topics covered

Bioinformatics, Data handling, Data mining, Data visualisation, Genomics, Sequence variations


After this course you should be able to:

  • Recognize the challenges and pitfalls of the analysis of human genome sequence variation
  • Recognize issues with the data
  • Visualize alignments and variants using a genome viewer
  • Evaluate the quality of your alignments and your variants
  • Understand the standard file formats for representing variant data
  • Apply filters to your list of variants
  • Functionally annotate variants

During this course you will learn about:

  • Introduction to genome variation
  • Experimental design
  • Genome sequence alignment
  • Data quality assessment
  • Variant calling
  • Variant filtering, effect prediction and prioritisation
  • Genome-wide association

Presentations, demonstrations and practicals


Day 1 Topics Speaker(s)
09:30 - 10:30 Introductory lecture on genetics, experimental design, NGS, Illumina and
other platforms
Marta Bleda, Matthias Haimel,
Stefan Graf
10:30 - 10:50 Hands-on introduction to iPython and Bash
10:50 - 11:00 Tea/Coffee Break
11:00 - 12:00 Lecture and hands-on session on Fastq QC

11:00 - 12:00 Lecture and hands-on session on Alignment with align reads over lunch
12:30 - 13:30 Lunch
13:30 - 14:00 Hands-on session on Alignment Marta Bleda, Matthias Haimel,
Stefan Graf
14:00 - 15:00 Lecture on Alignment towards sequence variation
15:00 - 15:10 Tea/Coffee Break
15:10 - 16:30 Hands-on session on Alignment/Variation
Day 2
9:30 – 10:50 Lecture and Hands-on on Variant Calling Marta Bleda, Matthias Haimel,
Stefan Graf
10:50 - 11:00 Tea/Coffee Break
11:00 - 11:30 Lecture on Annotation and Prioritization
11:30 - 12:30 Hands-on on Annotation and Filtering
12:30 - 13:30 Lunch
13:30 - 15:00 Lecture and hands-on on Association Marta Bleda, Matthias Haimel,
Stefan Graf
15:00 - 15:30 Tea/Coffee Break
15:30 - 16:30 Own data analysis and troubleshooting
Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here

2 days


A number of times per year

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Events available