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Bioinformatics Workshop on S. aureus-related genomics topics

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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)
pdf tutorial-NGS
Thursday
Data processing, statistical tests (t-test, KS-test, Wilcoxon rank test for
Alere-Chip data from Africa project)
pdf tutorial-data-processing
data
file-1
file-2
Friday
Clustering methods, functional annotation with David (gene ontology)
(Alere Chip data from Africa project)
pdf tutorial-clustering
file-1

 

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