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Porubsky, D.* ; Sanders, A.D.* ; Taudt, A. ; Colomé-Tatché, M. ; Lansdorp, P.M.* ; Guryev, V.*

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

Bioinformatics, accepted (2019)
DOI Verlagsversion bestellen
: Verlagsversion online verfügbar 01/2021
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: R/Bioconductor package https://bioconductor.org/packages/breakpointR.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
ISSN (print) / ISBN 1367-4803
Zeitschrift Bioinformatics
Verlag Oxford University Press
Verlagsort Oxford
Begutachtungsstatus