Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

作者：Readman Chiu, Indhu‐Shree Rajan‐Babu, Jan M. Friedman, İnanç Birol · 发表于：Genome biology · 年份：2021 · DOI：10.1186/s13059-021-02447-3 · 被引用次数：116 · 研究领域：Genomics and Phylogenetic Studies、RNA and protein synthesis mechanisms、Genetic Neurodegenerative Diseases

Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing.