Why Unix?

There was a time when Excel spreadsheets were a legitimate tool for bioinformatics, but those days are long past. Sequencing runs produce massive quantities of data that must be moved from the sequencing facility to some place where you have plenty of data and processing power to complete your analysis. Unix-like operating systems are the de facto standard for almost all bioinformatics. I suggest you read the "Unix philosophy" (https://en.wikipedia.org/wiki/Unix_philosophy) to understand why this is so.

Our students must learn to use existing tools as well as create new programs to analyze data. Sometimes a new "tool" is just a simple shell script that chains together commands, but sometimes it is a suite of programs using shell, R, Perl, Python, and third-party binaries. To that end, half of our course is dedicated to teaching students about Unix, programming, and how to create and run pipelines.