DNA methylome analysis using short bisulfite sequencing data

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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles (2012, background): “[20] for a review and comparison between aligners).”
A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics (2013, methodology): “There are two approaches for mapping WGBS reads: the three-alphabet approach and the wild card approach [14].”
Analysing and interpreting DNA methylation data (2012, background): “A substitutions 38 and require special han‑ dling during bisulphite alignment as well as during the inference of absolute DNA methylation levels.”
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules (2012, background): “For this ‘‘directional’’ bisulfite library protocol, cytosine positions appear on the sequence reads as C or T depending on bisulfite conversion, whereas the complementary G on the strand opposite the C will only be read as G (Krueger et al. 2012).”
An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis (2013, background): “Trimming has been broadly adopted in most recent NGS studies, specifically prior to genome assembly [23], transcriptome assembly [24], metagenome reconstruction [25], RNA-Seq [26,27], epigenetic studies [7] and comparative genomics [28].”