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A unified framework to analyze transposable element insertion polymorphisms using graph genomes

Author

Listed:
  • Cristian Groza

    (McGill University)

  • Xun Chen

    (Kyoto University)

  • Travis J. Wheeler

    (University of Arizona)

  • Guillaume Bourque

    (Kyoto University
    McGill University
    Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University
    McGill University)

  • Clément Goubert

    (McGill University
    University of Arizona)

Abstract

Transposable elements are ubiquitous mobile DNA sequences generating insertion polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements insertions. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. Here, we demonstrate the versatility of GraffiTE by analyzing human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.

Suggested Citation

  • Cristian Groza & Xun Chen & Travis J. Wheeler & Guillaume Bourque & Clément Goubert, 2024. "A unified framework to analyze transposable element insertion polymorphisms using graph genomes," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53294-2
    DOI: 10.1038/s41467-024-53294-2
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