Genome Biology (Jul 2024)

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

  • Helyaneh Ziaei Jam,
  • Justin M. Zook,
  • Sara Javadzadeh,
  • Jonghun Park,
  • Aarushi Sehgal,
  • Melissa Gymrek

DOI
https://doi.org/10.1186/s13059-024-03319-2
Journal volume & issue
Vol. 25, no. 1
pp. 1 – 12

Abstract

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Abstract Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analysis, especially for long or complex repeats. Here, we introduce LongTR, which accurately genotypes tandem repeats from high-fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr and https://zenodo.org/doi/10.5281/zenodo.11403979 .

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