I am a student from the United States interested in writing a Master's thesis in Germany. I would really like to hear about the top graduate programs in bioinformatics programs in Germany in particular and Europe as a whole.
If you are particularly interested in studying (Bachelor, Master, PhD) and positions in Germany, have a look at the web site of the German Academic Exchange Service (DAAD):
Here is the search for Masters programs: https://www.daad.de/deutschland/studienangebote/international-programs/en/?p=l&q=°ree%5B%5D=2&subject=350&langDistribution=0 Enter "Bioinformatics" into the keyword field.
Information on doing your PhD in Germany: https://www.daad.de/deutschland/promotion/phd/en/ and search the PhD Database: https://www.daad.de/deutschland/promotion/phd/en/13306-phdgermany-database/
There is no specific filter for "Bioinformatics" therefore search through the results of "Mathematics/Natural sciences". I found http://wiki.techfak.uni-bielefeld.de/didy/Announcement as an example.
Have you considered the European Bioinformatics Institute (EBI) in the UK? There's information about our PhD programme here. We're part of EMBL, which also has research institutes in Heidelberg and Hamburg if you're particularly keen on staying in Germany, but note that they are mainly wet-lab institutes, so there will be fewer bioinformatics projects than at the EBI. If you do go for the EBI, there is a lot of interactions with the different EMBL sites as part of the PhD programme, which means you will visit Germany regularly.
I did my MSc at the University of Manchester. It is a good, well established programs. You don't really do that much research for an MSc in the UK. Mine was really only a semester project in the end so you have to look at the coursework too and see if they offer what you want.
But it's in Manchester, which is a pretty good city but not always as fun as was portrayed in 24 Hour Party People.