inquiSTR: New Toolkit Enables Rapid, Accurate Analysis of Tandem Repeats Across Populations
Researchers have introduced inquiSTR, a command-line toolkit capable of genotyping 1.78 million tandem repeat loci across the genome in under two minutes. Tandem repeats are highly mutable DNA sequences associated with a range of human traits and diseases, and analyzing them at population scale from long-read sequencing data has previously been computationally demanding. The tool's speed, accuracy, and built-in downstream analysis features could significantly accelerate large-scale genomic studies of repeat-associated conditions.
inquiSTR is a newly developed bioinformatics toolkit designed for fast, genome-wide tandem repeat (TR) length genotyping from population-scale long-read sequencing data. The tool leverages parallel processing and low-memory streaming algorithms to genotype a catalog of 1.78 million loci in less than two minutes, representing a substantial performance improvement over existing methods. Benchmarking against established tools and truth sets demonstrates both high accuracy and markedly faster runtime. Beyond genotyping, inquiSTR includes modules for downstream analyses including population structure inference, association testing, and outlier detection, making it a more comprehensive platform than simple genotyping tools. Tandem repeats are among the most mutable elements in the human genome and have been implicated in numerous diseases, including neurological and neuromuscular disorders. The toolkit is distributed as a command-line application, positioning it for integration into existing genomic analysis pipelines. Its efficiency at scale could enable researchers to include TR analysis in large biobank-level studies that were previously impractical.
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The preprint has not yet undergone peer review, so independent validation of the benchmarking claims is pending.
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- bioRxivCenter
inquiSTR: a toolkit for accurate and efficient population-scale tandem repeat genotyping and analysis
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