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Table 2 Alternative DNA methylation Analysis and Visualisation Tools

From: MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing

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

  1. EWAS epigenome-wide association studies using Illumina Infinium HM450 BeadArrays