Intro to practicals @ genomics course http://wurmlab.github.io/genomicscourse/2016-SIB/

1. Spring-school
in Bioinformatics
& Population Genomics
(practical sessions)

2. This changes
everything.
Any lab can
sequence
anything!

3. Genomics is taking over biology
• Applied:
• Cancer genomics
• Biodiversity assessments
• Stool microbiome sequencing
• Personalized medicine
• Research:
• Development,
• Evolution,
• Ecology
• … how life works!

4. BIG

7. PracticalsTeam
• Rob Waterhouse (Uni Geneva) - @rmwaterhouse
• Julien Roux (Uni Lausanne) - @_julien_roux
• Roddy Pracana (Queen Mary, London) @RoddyPracana
• Stefan Schiffels (Max Planck, Jena) @stschiff
• Yannick Wurm (Queen Mary, London) @yannick__

8. Practical sessions (Monday &Tuesday)
• Reads to reference genome & gene predictions:
• Short read cleaning,
• genome assembly,
• gene prediction,
• quality control.
• Population sequencing to genotypes to population genetics
statistics:
• Mapping reads, calling variants, visualizing variant calls.
• Analysing variants: PCA, measuring diversity &
differentiation.

9. Practical sessions (Weds &Thursday)
• Inferring population sizes and gene flow
• Gene expression:
• From raw sequencing data to transcript expression levels.
• Gene-level clustering and differential expression analysis.

10. Virtual Machine?

11. My favourite package?
• Already:
• Claudia Kasper: RMarkdown
• Michel Moser: Jupyter Notebook
• Sina Rüeger: R stuff
• Kevin Daly: tmux
• Maybe you?