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

Tools

Item Type:	Article
Title:	breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data
Creators Name:	Porubsky, D., Sanders, A.D., Taudt, A., Colomé-Tatché, M., Lansdorp, P.M. and Guryev, V.
Abstract:	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.
Keywords:	DNA Sequence Analysis, Software
Source:	Bioinformatics
ISSN:	1367-4803
Publisher:	Oxford University Press
Volume:	36
Number:	4
Page Range:	1260-1261
Date:	15 February 2020
Official Publication:	https://doi.org/10.1093/bioinformatics/btz681
PubMed:	View item in PubMed

Repository Staff Only: item control page