BISulfite-seq CUI Toolkit (BISCUIT) is a utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data. It was written to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data.
If you use BISCUIT, kindly cite:
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,
BISCUIT: an efficient, standards-compliant tool suite for simultaneous
genetic and epigenetic inference in bulk and single-cell studies,
Nucleic Acids Research, Volume 52, Issue 6, 12 April 2024, Page e32,
https://doi.org/10.1093/nar/gkae097
Instructions for downloading and installing BISCUIT can be found in the User Guide Download and Install page.
All releases of BISCUIT are available on GitHub.
Note, to use the BISCUIT QC script, the following tools must be installed and in
the user's PATH environment variable:
It is also useful to have dupsifter installed for marking duplicate reads during the alignment phase.
A User Guide has been created to provide useful documentation regarding the usage of BISCUIT. The guide can be found at: https://huishenlab.github.io/biscuit/.
Any issues with BISCUIT can be submitted on the Issues page: https://github.com/huishenlab/biscuit/issues.
- lib/aln was adapted from Heng Li's BWA-mem code.
- This work is supported by NIH/NCI R37CA230748 and U24CA210969.