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BISCUIT 
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.
Download and Install
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 samblaster installed for marking duplicate reads during the alignment phase.
Usage and Documentation
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/.
Issues
Any issues with BISCUIT can be submitted on the Issues page: https://github.com/huishenlab/biscuit/issues.
<!-- # Links --> <!-- - BISCUIT Publication --> <!-- > Link to publication -->Acknowledgements
- lib/aln was adapted from Heng Li's BWA-mem code.
- lib/htslib was subtree-ed from the htslib library.
- lib/klib was subtree-ed from Heng Li's klib.
- This work is supported by NIH/NCI R37CA230748 and U24CA210969.