breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data

David Porubsky*, Ashley D Sanders, Aaron Taudt, Maria Colomé-Tatché, Peter M Lansdorp, Victor Guryev

*Bijbehorende auteur voor dit werk

OnderzoeksoutputAcademicpeer review

8 Citaten (Scopus)
37 Downloads (Pure)

Samenvatting

Motivation: Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data. Results: Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique. Availability and implementation: R/Bioconductor package https://bioconductor.org/packages/breakpointR.

Originele taal-2English
Pagina's (van-tot)1260-1261
Aantal pagina's2
TijdschriftBioinformatics (Oxford, England)
Volume36
Nummer van het tijdschrift4
Vroegere onlinedatum30-aug-2019
DOI's
StatusPublished - 15-feb-2020

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