ArticleGenome biology2024
LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.Nature protocols · 2026Guideline
- Nanopore sequencing combined with adaptive sampling and NanoExpansion enables accurate characterization of repeat expansion disorders.NAR genomics and bioinformatics · 2026Article
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome.Bioinformatics (Oxford, England) · 2026Article
- Targeted long-read sequencing enables comprehensive analysis of the genetic and epigenetic landscape of inherited myopathies.Nature communications · 2026Article
- Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism.Cell genomics · 2026Article
- Long-read analysis of tetrameric microsatellites with vmwhere supports GGAA repeat length-dependent chromatin state association in Ewing sarcoma.bioRxiv : the preprint server for biology · 2026Article
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- Defining a tandem repeat catalog and variation clusters for genome-wide analyses.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes.bioRxiv : the preprint server for biology · 2026Article
- Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit.Genome research · 2026Article
- Structural variations in evolutionary novel genomic regions: new insights into neurodevelopmental disorders by long-read DNA Sequencing.Molecular medicine (Cambridge, Mass.) · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.Genome biology and evolution · 2026Review
- Alzheimer's disease: genetic background in the era of next-generation sequencing technologies.Brain communications · 2026Review
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms.Communications biology · 2025Article
- Population-scale Long-read Sequencing in themedRxiv : the preprint server for health sciences · 2025Article
- Diverse short tandem repeat sequences influence gene regulation in human populations.Genome biology · 2025Article
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6 authors.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.