BisPin and BFAST-Gap
BisPin is a Python 2.7 program that uses BFAST-Gap (or BFAST) to map bisulfite-treated short DNA reads to a reference genome. It supports the hairpin construction strategy and rescores ambiguously mapped reads. Its default alignment scoring function is biologically motivated.
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BisPin and BFAST-Gap: Mapping Bisulfite-Treated Reads
Jacob Porter, Liqing Zhang
bioRxiv 284596; doi: https://doi.org/10.1101/284596