Disclaimer

We will introduce a plethora of individual software tools in the course of this Wiki and the practical work. These tools are just a small selection from the universe of alternative software solutions all addressing more or less the same problem. Keep in mind that the tools that we propose are not necessarily the optimal choice for our analysis. Keep your eyes open for alternative software that might do a job better than our choice. To simplify the work with these tools, we provide in many instances examples of how to call these programs via the command line. Please bear in mind that:

Tools evolve sometimes more quickly than we can update this Wiki, although we try to avoid this to the best possible extent. If it still happens that a program call does not work at all, please inform us, such that we can update the call to the newest version.
In some instances, the example program call may contain parameter values that might not be optimal or not even appropriate for your particular data set and analysis.
Formatting may make the program call look differently in the script than it looks in the terminal.

In essence, rather than just copy-pasting the program tools, make sure to understand what information is passed on to the program and adapt it to your needs.