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.
Communication, questions, etc...
If you want to contact us please reach out in our MS teams (rather than writing an email to a specific person). It makes it easier for us to see and answer your questions.
Getting started
For connecting to ScienceCluster as well as writing your scripts, we recommend you download Visual Studio Code for Mac and Windows (https://code.visualstudio.com/download). You will also need to install the extension "Remote - SSH" to connect via SSH.
Connecting
Open VSCode and click on the green >< symbol in the lower left corner. Then select Connect to Host, Add new SSH Host and then type
ssh <username>@cluster.s3it.uzh.chNOTE: You need to be in the UZH VPN in order to connect to ScienceCluster. Please follow the instructions here: External UZH Network Access (VPN)
Other software
Tablet for visualising NGS assemblies (https://ics.hutton.ac.uk/tablet/) or 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
AliView (http://www.ormbunkar.se/aliview) - Lightweight viewer for multiple sequence alignments
Course material
- Introduction to the projects
- Introduction to NGS and routine diagnostics
- NGS technologies
- ONT Library preparation
- Intro to NGS QC