Next-Generation Sequencing technologies combined with a bisulfite treatment of DNA (BS-Seq) present an efficient method in the field of epigenomics, allowing for a precise analysis of methylation patterns at single-nucleotide resolution. The expanding field leads to the production of enormous amounts of data, that need to be analysed using precise and efficient software tools. The analysis needs to address the specific challenges arising from the bisulfite treatment, which converts unmethylated Cs to Ts. We present a powerful analysis workflow, implemented using the C++ software library SeqAn, for accurate bisulfite read mapping, the detection of single-nucleotide polymorphisms and methylation level calling at single-nucleotide resolution. Furthermore, we provide a multiple sequence realignment method to improve the alignment accuracy for indel reads. We show that in comparison to existing methods, we achieve comparable and even better results.