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Table 2 Bioinformatics tools for bisulfite sequencing data analysis

From: Profiling genome-wide DNA methylation

Function(s) Software Features References
Quality trim Cutadapt Removes adapter sequences [92]
Bisulfite sequencing aligner Bismark Three-letter aligner; supporting both Bowtie and Bowtie2 [96]
BRAT-BW Three-letter aligner for mapping and methylation calling [97]
BS Seeker 2 Three-letter aligner; supporting local alignment, and computational removal of unconversion reads [98]
MethylCoder Three-letter aligner to be used with Bowtie or GSNAP [99]
GSNAP Wild card aligner [100]
LAST Wild card aligner wrapped in a general-purpose alignment tool [101]
Data visualization UCSC Genome Browser Web-based genome browser allowing visualizing DNA methylation data ( [104]
WBSA Web service for comprehensive analysis of WGBS and RRBS data and DMR finding ( [105]
Integrative Genome Viewer (IGV) Graphical genome browser to run locally on the user’s computer [106]
Methylation plotter Web-based tool that plot up to 100 samples in lollipop or grid style ( [107]
Post-alignment data analysis BSPAT  Summarizing and visualizing DNA methylation co-occurrence patterns
 Detecting allele-specific methylation
 Performing integrative analysis with genomic features such as histone modification
GBSA  Sequencing quality assessment
 Methylation level scoring
 Data management and visualization
MethGo  Calculating and plotting global methylation level
 Genome-wide methylation plot
 Calculating methylation level in different genomic regions
 Extracting SNP and CNV information from BS-seq data
 Profiling methylation at transcriptional factor binding sites
SAAP-RRBS  Read quality assessment
 Alignment and methylation calling
 CpG annotation and reporting for high coverage and quality CpGs that could be visualized with IGV
SMAP  Read quality assessment
 Alignment and methylation calling
 Differentially methylated cytosine detection with Chi-square test and DMR calling by Fisher’s exact test
 Detecting SNPs and allele-specific methylation
Identifying DMR BSmooth A pipeline includes alignment, quality control and data analysis; the DMR finding function adapts bump hunting on smoothed t-like score; supporting multiple testing correction [110]
methylKit R package for clustering, sample quality visualization and DMR finding with logistic regression; supporting multiple testing correction [112]
methylSig R package for DMR finding with likelihood ratio test; supporting multiple testing correction [113]
methylPipe R package for DMR finding with Wilcoxon or Kruskal–Wallis paired nonparametric test; supporting multiple testing correction [114]
BiSeq R package for DMR finding with Wald test; performing comprehensive RRBS data analysis; supporting multiple testing correction [115]
  1. BRAT-BW Bisulfite-treated Reads Analysis Tool (Burrows–Wheeler transform), UCSC genome browser University of California Santa Cruz Genome Browser, WBSA web service for bisulfite sequencing data analysis, BSPAT bisulfite sequencing pattern analysis tool, GBSA genome bisulfite sequencing analyser, IGV integrative genomics viewer, SAAP-RRBS streamlined analysis and annotation pipeline for RRBS data, SMAP streamlined methylation analysis pipeline