Lecturer: Prof. Dr. Volkhard Helms
Tutors: Ruslan Akulenko, Mohamed Hamed Ali Fahmy, Kerstin Reuter
Date: Monday, August 25 – Friday, August 29
Time: 9:30 am – 12:00 am and 2:00 pm – 4:30 pm
This workshop has been sponsored by the DFG.
Program:
| Monday: | Introduction to databases NCBI/EBI, UCSC genome browser, Patric and basic sequence alignment with BLAST (single sequences of resistance marker genes, e.g. MecA, PVL of different S. aureus strains) |
pdf-Intro pdf-BLAST |
tutorial-databases file-1 file-2 file-3 |
| Tuesday | Multiple sequence alignment, phylogenies (data from WGS project on invasive/ non-invasive t003/t504 strains, core-genome approach) |
pdf-MultSeqAlign pdf-phylogeny |
tutorial-phylogeny |
| Wednesday | Genome assembly, mapping of reads against reference genomes, SNP calling (data from WGS projecton invasive/non-invasive t003/t504 strains, core-genome approach) |
tutorial-NGS | |
| Thursday | Data processing, statistical tests (t-test, KS-test, Wilcoxon rank test for Alere-Chip data from Africa project) |
tutorial-data-processing data file-1 file-2 |
|
| Friday | Clustering methods, functional annotation with David (gene ontology) (Alere Chip data from Africa project) |
tutorial-clustering file-1 |