Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
Abstract 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 expansio...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-08-01
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| Series: | Genome Biology |
| Online Access: | https://doi.org/10.1186/s13059-021-02447-3 |
| Summary: | Abstract 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. |
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| ISSN: | 1474-760X |