Table 1.

Advantages and disadvantages of different categories of automation strategies for bioinformatics

	Advantages	Disadvantages
Scripting	∙ Simple to construct	∙ Hard to hand over, manual tools integration and difficult HPC interaction
Makefile	∙ Simple to construct once you are familiar with the programming languages and the bioinformatics command-line tools involved	∙ Multithreaded programs and remote execution not handled well
	∙ Describes data flow and takes care of dependency resolution, parallel execution and caching results from previous runs	∙ Lack of recursion support
	∙ Uses code fragments in familiar scripting languages for processing of data	∙ Requires programming or shell experience
		∙ Can’t be automatically parsed and visualized
Scientific Workflow Systems	∙ More powerful features, easier to maintain and share	∙ Requires more effort