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Medientyp:
E-Artikel
Titel:
breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data
Beteiligte:
Porubsky, David;
Sanders, Ashley D;
Taudt, Aaron;
Colomé-Tatché, Maria;
Lansdorp, Peter M;
Guryev, Victor
Erschienen:
Oxford University Press (OUP), 2020
Erschienen in:Bioinformatics
Sprache:
Englisch
DOI:
10.1093/bioinformatics/btz681
ISSN:
1367-4803;
1367-4811
Entstehung:
Anmerkungen:
Beschreibung:
<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Motivation</jats:title>
<jats:p>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.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>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.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Availability and implementation</jats:title>
<jats:p>R/Bioconductor package https://bioconductor.org/packages/breakpointR.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Supplementary information</jats:title>
<jats:p>Supplementary data are available at Bioinformatics online.</jats:p>
</jats:sec>