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:10.1186/s13059-024-03319-2

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

Genome Biol. 2024 Jul 4;25(1):176. doi: 10.1186/s13059-024-03319-2.

Authors

Helyaneh Ziaei Jam¹, Justin M Zook², Sara Javadzadeh¹, Jonghun Park¹, Aarushi Sehgal¹, Melissa Gymrek^{3

4}

Affiliations

¹ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
² Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, USA.
³ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. mgymrek@ucsd.edu.
⁴ Department of Medicine, University of California San Diego, La Jolla, CA, USA. mgymrek@ucsd.edu.

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 .

Keywords: Long reads; Microsatellites; Tandem repeats.

MeSH terms

Genetic Variation*
Genome, Human*
High-Throughput Nucleotide Sequencing / methods
Humans
Nanopore Sequencing / methods
Sequence Analysis, DNA / methods
Software
Tandem Repeat Sequences*

Abstract

MeSH terms

Grants and funding