Table 1 Summary of bioinformatic tools for data analysis using aligned BS-seq.
From: MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data
| Â | MethGo | Kismeth[16] | Bis-SNP[17] | GBSA[18] | Repitools[19] | ReadDepth[20] |
|---|---|---|---|---|---|---|
Programming Language | Python | unknown | Java | Python | R | R |
Operating System | Windows/ Unix | web | Windows/ Unix | Windows/ Unix | Windows/ Unix | Unix |
Interface | Command-line | GUI | Command-line | GUI/ Command-line | Command-line | Command-line |
Coverage distribution | Yes (*F) | - | - | - | Yes | - |
Global cytosine methylation level | Yes (*F) | Yes | - | - | - | - |
Cytosine methylation level distribution | Yes (*F) | - | - | - | - | - |
Cytosine methylation level of genomic elements | Yes (*F) | - | - | - | - | - |
Chromosome-wide cytosine methylation level distribution | Yes (*F) | - | - | - | - | - |
Gene-centric cytosine methylation level | Yes (*T) | - | - | Yes | - | - |
Cytosine methylation level of TFBSs | Yes (*F) | - | - | - | - | - |
SNP calling | Yes (*T) | - | Yes | - | - | - |
CNV calling | Yes (*F) | - | - | - | - | Yes |
Main functions of tool | Methylation profiling and extracting genetic variation information from bisulfite sequencing data | Global methylation levels calculation and visualization at nucleotide resolution | SNP calling | Gene-centric methylation level scoring and visualizetion | Enrichment based epigenomic data analysis such as coverage distribution of CpG sites | CNV calling |