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

Genome Biol. 2021 Aug 13;22(1):224. doi: 10.1186/s13059-021-02447-3.


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.

Publication types

  • Research Support, Non-U.S. Gov't

Grant support