Table 1.

Summary of the programs included in HBS-tools.

Module name	Function
hbs_process	Preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal
hbs_mapper	Original sequence recovery, mapping, and SAM file output
hbs_methylation_extractor	Extract and output methylation pattern from the SAM file
hbs_cg_mlmf	Summarize the methylation level and fidelity for covered CpG sites
hbs_ch_ml	Summarize the methylation level for covered non_CpG sites