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Updated: Feb 8, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data
Panisa Treepong1,2, Christophe Guyeux1, Alexandre Meunier3,4
1Département DISC, UMR CNRS 6174 Institut FEMTO-ST, Université de Bourgogne, Franche-Comté, Besançon, France.
Motivation:
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.
Results:
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 https://github.com/bvalot/panISa.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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