ArticleGenome biology2022
STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 57 citations in OpenAlex.
- Genome-wide detection and clinical prioritization of tandem repeat outliers using long-read sequencing.medRxiv : the preprint server for health sciences · 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
- ntStat: k-mer characterization using occurrence statistics in raw sequencing data.PLoS computational biology · 2026Article
- Defining a tandem repeat catalog and variation clusters for genome-wide analyses.bioRxiv : the preprint server for biology · 2026Article
- Short tandem repeat expansions in patients with neurodegenerative dementia.EBioMedicine · 2026Article
- A comprehensive tandem repeat catalog of the human genome.Nature communications · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Detection of short tandem repeat expansions on a targeted neurological gene panel using STRipy improves the diagnostic rate for ataxias.Brain communications · 2026Article
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- Genotyping TOMM40'523 poly-T polymorphisms using whole-genome sequencing.HGG advances · 2025Article
- Additional Diagnostic Yield through the Analysis of Short Tandem Repeats Based on Exome Sequencing Data.The Journal of molecular diagnostics : JMD · 2025Article
- STRaM: A genetic framework for improved cell product provenance for research and clinical translations.Communications biology · 2025Article
- A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort.Genetics in medicine : official journal of the American College of Medical Genetics · 2025Article
- Review
- The Utah NeoSeq Project: a collaborative multidisciplinary program to facilitate genomic diagnostics in the neonatal intensive care unit.NPJ genomic medicine · 2025Article
- ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads.bioRxiv : the preprint server for biology · 2025Article
- Review
- Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer's disease.Nature communications · 2025Article
- Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.Nucleic acids research · 2025Article
- Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease.Nucleic acids research · 2025Review
Corrections and comments
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Authors and funding
14 authors at 9 institutions in 4 countries.
Funding
Abstract
Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for "novel" STRs, which include new motifs at known loci or STRs absent from the reference genome. We developed STRling to efficiently count k-mers to recover informative reads and call expansions at known and novel STR loci. STRling is sensitive to known STR disease loci, has a low false discovery rate, and resolves novel STR expansions to base-pair position accuracy. It is fast, scalable, open-source, and available at: github.com/quinlan-lab/STRling .
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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.