The popular Sequence Alignment Map format, SAM, has given rise to an equally popular toolkit for working with SAM files (and BAM, CRAM too). But what is the name of this tool?

SAMtools?

If we read the official publication, then we see this software described as 'SAMtools' (also described by Wikipedia in this manner).

Samtools?

Head to the official website and we see consistent references to 'Samtools'.

samtools?

Head to the official GitHub repository and we see consistent references to 'samtools'.

This is not exactly a problem that is halting the important work of bioinformaticians around the world, but I find it surprising that all of these names are in use by the people that developed the software. Unix-based software is typically — but not always — implemented as a set of lower-case commands and this can add one level of confusion when comparing a tool's name to the actual commands that are run ('samtools' is what you type at the terminal). However, you can still be consistent in your documentation!