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The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output of each coding sequence with corresponding mapped insertions accompanied with normalised results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritising results for further investigation.Availability: The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS