BiQ Analyzer HT is a user-friendly software tool for sequence alignment, quality control and initial analysis of locus-specific DNA modification data. In particular, BiQ Analyzer HT is intended for analyzing medium-scale amplicon sequencing data (typically using MiSeq). The software supports four different assay types, and it leads the user from raw sequence reads to DNA modification statistics and publication-quality plots. The software facilitates the shift from time-consuming clonal bisulfite sequencing to the more quantitative and cost-efficient use of high-throughput sequencing for studying locus-specific DNA methylation patterns. BiQ Analyzer HT is also useful for locus-specific visualization of genome-wide bisulfite sequencing data.