BiQAnalyzer HT is the major upgrade of the popular BiQAnalyzer tool specifically designed to aid the analysis of high-throughput bisulfite amplicon sequencing data. BiQAnalyzer HT currently allows to process an amount of bisulfite sequencing reads obtained in one or several bisulfite sequencing experiments.
Becker D., Lutsik P., Ebert P., Lengauer T. and Walter J. (2014) BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives. Nucleic Acids Research (Full text).