Table 7.
Bioinformatics tools for the analysis of bisulfite sequencing data.
| Tools | Descriptions | Reference |
|---|---|---|
| BiQ Analyzer HT | Quantitative study of locus-specific DNA methylation patterns from bisulfite sequencing data. | [166] |
| Bismark | Mapping of bisulfite-sequencing reads and methylation calling. | [167] |
| BRAT-BW | Genome-wide single base-resolution methylation data analysis | [168] |
| BSmooth | Providing estimate of methylation profiles with low-coverage whole-genome bisulfite-sequencing data. | [169] |
| BS seeker | Mapping of bisulfite-sequencing reads. | [170] |
| BSMAP | Bisulfite reads mapping algorithm. | [171] |
| CpG_MPs | Analysis of biosulfite-sequencing read and identification of genome-wide methylation pattern | [172] |
| GBSA | Both gene-centric or gene-independent analyses of whole-genome bisulfite sequencing data | [173] |
| Kismeth | Analysis of plant bisulfite sequencing results, with a tool for designing bisulfite sequencing primers. | [174] |
| QUMA | Quantification tool for methylation analysis | [175] |
| RRBSMAP | Derivative of BSMAP—a specific tool for reduced-representation bisulfite sequencing | [176] |