Table 2 Bioinformatics tools for bisulfite sequencing data analysis
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 (https://genome.ucsc.edu) | [104] |
WBSA | Web service for comprehensive analysis of WGBS and RRBS data and DMR finding (http://wbsa.big.ac.cn/) | [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 (http://gattaca.imppc.org:3838/methylation_plotter) | [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 | [108] |
GBSA |  Sequencing quality assessment  Methylation level scoring  Data management and visualization | [93] | |
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 | [109] | |
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 | [94] | |
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 | [95] | |
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] |