Spring-school in Bioinformatics & Population Genomics

(practical sessions)

This changes everything.

Any lab can sequence anything!

Genomics is taking over biology• Applied:

• Cancer genomics• Biodiversity assessments• Stool microbiome sequencing• Personalized medicine

• Research: • Development, • Evolution, • Ecology• … how life works!

DATABIG

Practicals Team

• 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__

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.

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.

Virtual Machine?

My favourite package?• Already:

• Claudia Kasper: RMarkdown

• Michel Moser: Jupyter Notebook

• Sina Rüeger: R stuff

• Kevin Daly: tmux

• Maybe you?