Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes. Aligning bisulfite-treated reads, however, is a computationally difficult task: bisulfite treatment decreases the (lexical) complexity of low-methylated genomic regions, and C-to-T mismatches may reflect cytosine unmethylation rather than SNPs or sequencing errors. Further challenges arise both during and after the alignment phase: data structures used by the aligner should be fast and should fit into main memory, and the methylation-caller output should be somehow compressed, due to its significant size.