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Fanny Wegner authoredFanny Wegner authored
Blockkurs Microbial Bioinformatics
Welcome to the home page of the Microbial Bioinformatics course. You can find and exercise instructions here (uploaded as we go along) as well as software that should be installed beforehand.
Getting started
Windows
Please download and install this command line tool to connect to Science Cluster.
MobaXTerm (http://mobaxterm.mobatek.net/)
A simple editor for code writing is for example Notepad++ (https://notepad-plus-plus.org).
Macintosh
There is already an application called Terminal installed on your system. However, we recommend installing Termius (https://termius.com/download/macos) for easier file transfer to and from Science Cluster. You will have to create an account (or sign in with Google/Apple), but it's free.
A simple editor with syntax highlighting would be for example BBEdit which you can install via the App Store.
Other software
IGV Integrative Genomics Viewer (https://software.broadinstitute.org/software/igv/home)
Figtree (https://github.com/rambaut/figtree/releases) - Software to visualise phylogenetic trees. Please download and unpack/install the
- zip for Windows
- dmg for MacOS
- tgz for Linux
Bandage (https://rrwick.github.io/Bandage/) - Software to visualise assembly graphs
Course material
- Welcome from Director of the IMM
- Introduction to the projects
- Introduction to NGS and routine diagnostics
- NGS technologies
- Intro to NGS QC