The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data.


PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic species Pseudomonas aeruginosa, and report 43 insertions of five different ISs (among which three are new) and a burst of ISPa1635 in a hypermutator isolate.

Availability and implementation

PanISa is implemented in Python and released as an open source software (GPL3) at

Supplementary information

Supplementary data are available at Bioinformatics online.

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