Monday: 2-8 pm Berlin time. The basics of genome scale analyses

Lecture 1

-       General introduction

-       File formats: FastQ, SAM, BAM, GFF3

-       Introduction in de novo assembly strategies, best practices and quality control

Lab 1

-       Setting up the computers/AWS instances

-       Reads QC + trimming

-       First steps in genome assembly

 

Tuesday: 2-8 pm Berlin time. de novo Genome Assembly

Lecture 2

-    De novo assembly 2: Discussion and next steps

Lab2

-       run your own de novo genome assembly (short + long read based)

-       Computation and interpretation of assembly summary statistics

 

Wednesday: 2-8 pm Berlin time. Genome annotation and gene set completeness analysis

Lecture 3

-       The annotation of eukaryotic genomes

·         Repeat annotation

·         Gene identification

·         Gene order and shared synteny

Lab 3

-       Genome annotation using the Maker2 pipeline

-       Setting up a genome browser (IGV)

-       Gene set completeness analysis

-       Analysis of shared synteny

 

Thursday: 2-8 pm Berlin time. Comparative Genomics - Run a multi sample SVs comparison

Lecture 4

-       What are SVs and why are they important?

-       Read Mapping - The basis of SV calling

-       Concepts and methods of SV calling

Lab 4

-       How to choose the appropriate short read mapper?

-       Calling of SVs using de-novo and mapping based approaches

-       Comparison of de novo based and mapping based results

-       SV quality control

 

Friday: 2-8 pm Berlin time. Predicting the functional consequences of genomic variations

Lecture 5

-       Assessment of gene function (e.g. GO analysis)

-       Functional changes due to loss, SVs, cis-regulation

-       Impact in pathways (e.g. KEGG)

Lab 5:

-       Functional annotation of variants

-       Identification of orthologs/homologs across species

-       GO annotation and analysis

-       Running your own pathway analysis

Lecture 6:

-     Summary and discussion