intmap: Fast and Flexible Mapping of Mobile DNA Integration for Basic and Translational Research

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ID: 314050
2026
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Abstract
Abstract Summary Integration of exogenous DNA into host cell chromatin is a hallmark of many virus and transposon lifecycles and the foundational basis for many modern cellular and genetic therapies. Defining integration sites (ISs) in a population of cells can accordingly inform fundamental aspects of mobile DNA biology and therapeutic treatment outcomes. Here, we describe intmap, a software that generalizes IS analysis to diverse data-types and experimental systems. intmap functions independently of strict library design assumptions and is highly tunable with respect to analysis parameters. Using both simulated and experimental data, we show that IS mapping with intmap is fast, accurate, and highly flexible. Availability and implementation intmap, related documentation, and a convenient installation script are available at https://github.com/gbedwell/intmap. Additional information is provided in the online Supplement. Analysis commands, outputs, and other information related to this manuscript are available at https://doi.org/10.5281/zenodo.19475929.
Reference Key
openalex_W7161573572 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Gregory J. Bedwell, P.G. Cherepanov, Alan N Engelman
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag310
URL
https://doi.org/10.1093/bioinformatics/btag310
Keywords Keywords not found

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