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Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences Chiu, Readman; Rajan-Babu, Indhu-Shree; Friedman, J. M. (Jan Marshall), 1947-; Birol, Inanc

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.

Item Metadata

Title
Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
Creator
Chiu, Readman; Rajan-Babu, Indhu-Shree; Friedman, J. M. (Jan Marshall), 1947-; Birol, Inanc
Contributor
Michael Smith Genome Sciences Centre; BC Cancer Agency; Children's Hospital (Vancouver, B.C.). Research Institute
Publisher
BioMed Central
Date Issued
2021-08-13
Description
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.
Genre
Article
Type
Text
Language
eng
Date Available
2021-09-02
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0401870
URI
http://hdl.handle.net/2429/79609
Affiliation
Medicine, Faculty of; Non UBC; Medical Genetics, Department of
Citation
Genome Biology. 2021 Aug 13;22(1):224
Publisher DOI
10.1186/s13059-021-02447-3
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
The Author(s)
Rights URI
http://creativecommons.org/licenses/by/4.0/
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DSpace

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Rights

Attribution 4.0 International (CC BY 4.0)