Software: Snakemake


Snakemake is the build system, similar to GNU Make. Can be used to create complicated workflows. Although it can be used as a generic workflow scripting tool, it has been developed and mostly used for bioinformatics pipelines. The program uses its own domain specific language (DSL) very similar and inspired by Python programming language. Its advantage over Make is ease of use. It is especially attractive choice for Python programmers. It can be used whenever the workflow consists of multiple steps (rules). Results are piped from one rule to another, giving in the end a pipeline. Snakemake interfaces with Python and R. Both languages can be used directly within the rule specification. In bioinformatics Snakemake is often used to combine together subsequent steps in DNA sequencing data analysis.

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