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

Porubsky, D., Sanders, A. D., Taudt, A., Colomé-Tatché, M., Lansdorp, P. M. & Guryev, V., 30-Aug-2019, In : Bioinformatics (Oxford, England).

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

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DOI

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.

Original languageEnglish
JournalBioinformatics (Oxford, England)
Publication statusE-pub ahead of print - 30-Aug-2019

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