TRIUMPH Microbial Genomics course: Setup

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they’re working. If you have any problems, don’t hesitate to email the instructors to ask for help, or arrive early on the first day to get help.

Web browser

• Go to the Chrome download page
• Click and the button and install Chrome
• Other browsers will likely work as well but no guarantees

MinKNOW - not necessary for the course but useful for setting up your own bioinformatics pipeline

For basecalling, MinKNOW can be used. MinKNOW is the basecalling package of Oxford Nanopore Technologies that allows you to basecall and demultiplex your samples. If you want to install MinKNOW on Windows, please follow these instructions: Link

Epi2me - not necessary for the course but useful for setting up your own bioinformatics pipeline

For some tasks Epi2me can be used. Epi2me is the analysis package of Oxford Nanopore Technologies that allows you to run various bioinformatics pipelines without installing a linux system. Tasks such as assembly and/or MLST and resistance gene detection can be performed. If you want to install Epi2me, please follow these instructions: Link