Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences.
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
13 08 2021
13 08 2021
Historique:
received:
03
02
2021
accepted:
26
07
2021
entrez:
14
8
2021
pubmed:
15
8
2021
medline:
20
1
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34389037
doi: 10.1186/s13059-021-02447-3
pii: 10.1186/s13059-021-02447-3
pmc: PMC8361843
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
224Subventions
Organisme : CIHR
ID : 16907
Pays : Canada
Informations de copyright
© 2021. The Author(s).
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