Transposon insertion mapping with PIMMS - Pragmatic Insertional Mutation Mapping System.
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 normalized results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritizing results for further investigation.


BACKGROUND
The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS.
School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK.
Adam M
AM
Blanchard
School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK.
James A
JA
Leigh
School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK.
Sharon A
SA
Egan
School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK.
Richard D
RD
Emes
INseq; TnSeq; TraDIS; sequencing; transposon mapping