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

被引：36

作者：

Chiu, Readman ^{[1
]}

Rajan-Babu, Indhu-Shree ^{[2
,3
,4
]}

Friedman, Jan M. ^{[2
,3
]}

Birol, Inanc ^{[1
,2
]}

机构：

[1] BC Canc, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada

[2] Univ British Columbia, Dept Med Genet, Vancouver, BC V6T 1Z3, Canada

[3] BC Childrens Hosp Res Inst, Vancouver, BC V5Z 4H4, Canada

[4] Kings Coll London, Dept Med & Mol Genet, London WC2R 2LS, England

来源：

GENOME BIOLOGY | 2021年 / 22卷 / 01期

基金：

加拿大健康研究院;

关键词：

D O I：

10.1186/s13059-021-02447-3

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：20

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