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breakpointR: An R/Bioconductor package to localize strand state changes in Strand-seq data.
Bioinformatics 36, 1260-1261 (2020)
Publ. Version/Full Text
Research data
DOI
PMC
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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Publication type
Article: Journal article
Document type
Scientific Article
ISSN (print) / ISBN
1367-4803
e-ISSN
1367-4811
Journal
Bioinformatics
Quellenangaben
Volume: 36,
Issue: 4,
Pages: 1260-1261
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Computational Biology (ICB)