Software | Program Language and Implementation | Analysis Process | Visual Output | Input file | Output file | Epiallelic Counts | Experiment Quality Check |
---|---|---|---|---|---|---|---|
Methpat | Python, pip install, URL available to install files locally | Summarises Bismark output | Interactive HTML and summary text file of epiallele counts. Scalable PNG file | Bismark methylation extractor output, user-defined BED format file | HTML and tab delimited text file | Yes | No, leverages Bismark |
Bismark | command line,Python, requires bwa | Performs alignment to bisulfite reference genome | None, generates BAM files for visualisation with SeqMonk or IGV | fastq file | BAM and tab deliminted text files | No | Yes calculates C to T conversion |
BSPAT | Java/JSP web interface | Visualisation and summarisation of Bismark output | PNG file and UCSC Genome Browser file | Bismark output, fastq files | Text file summary, PNG and UCSC Genome Browser BED file | Yes | No |
MPFE | R library, Bioconductor | Calculates probabilities that epialleles are true | R image outputs | Table of read counts from bisulfite sequencing data | Derived statistics and plots | Yes | Yes |
Methylation plotter | R library, shiny interactive web application | Visualises beta DNA methylation values | Interactive webpage with setting options to adjust a static image of DNA methylation values for each sample. PNG and PDF output. | Text file containing matrix of sample vs beta value at each CpG of interest | PDF and PNG image file | No | No |
RnBeads | R library, Bioconductor | Processes summary data from other software for visualisation | Interactive HTML and UCSC Genome browser track hub files. PNG files | BED file | HTML summary | No | Yes |
coMET | R library, Webserver for analysis | For EWAS studies. Analyses derived matrix files | Image files of plots with genomic locations. | Text matrix files | Image files | No | No |