Here is the key point: > elPrep allows users to specify arbitrary combinations of SAM/BAM operations as a single pipeline in one command line. The assumption

Here is the key point: > elPrep allows users to specify arbitrary combinations of SAM/BAM operations as a single pipeline in one command line. The assumption is that your native environment for data analysis is bash and you have to expose anything that you might want to do in bash. Further, > elPrep also accommodates functional steps provided by third-party tool writers That is, they are attempting to provide general semantics in a bash command line that they can handle arbitrary functions being dropped into their program. Remember, the average salary of a job requiring both programming and biology knowledge is much lower than the average salary of a job requiring programming knowledge alone, so as bioinformaticists build skill to the point where they can be employable as programmers, they mostly leave bioinformatics. Those who have escaped bash have usually done so into Python these days, which creates a class system of those gluing things together in Python versus those implementing algorithms in C or C++.