BISCUIT: An efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies

Wanding Zhou, Benjamin K. Johnson, Jacob Morrison*, Ian Beddows, James Eapen, Efrat Katsman, Ayush Semwal, Walid Abi Habib, Lyong Heo, Peter W. Laird, Benjamin P. Berman, Timothy J. Triche, Hui Shen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient mapping of methylation sequencing reads, routinely discarded genetic information, and neglected read-level epigenetic and genetic linkage information. We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing. BISCUIT's performance, flexibility and standards-compliant output allow large, complex experimental designs to be characterized on clinical timescales. BISCUIT is particularly suited for processing data from single-cell DNA methylation assays, with its excellent scalability, efficiency, and ability to greatly enhance mappability, a key challenge for single-cell studies. We also introduce the epiBED format for single-molecule analysis of coupled epigenetic and genetic information, facilitating the study of cellular and tissue heterogeneity from DNA methylation sequencing.

Original languageAmerican English
JournalNucleic Acids Research
Volume52
Issue number6
DOIs
StatePublished - 12 Apr 2024

Bibliographical note

Publisher Copyright:
© 2024 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

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