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Data visualization software tools | Bisulfite sequencing data analysis

While some software tools to analyze and visually represent DNA methylation data have been published (reviewed in Laird, 2010), its use by wet lab users is often limited. On the other hand, popular spreadsheet tools like Excel are unable to generate…
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WashU…
Web

WashU Epigenome Browser

A genome browser focusing on the human epigenome. The Browser is web-based and…

A genome browser focusing on the human epigenome. The Browser is web-based and it extends the seminal concept invented by the UCSC Cancer Genomics Browser to support large, sequencing-based datasets.…

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SeqMonk
Desktop

SeqMonk

A program to enable the visualisation and analysis of mapped sequence data.…

A program to enable the visualisation and analysis of mapped sequence data. SeqMonk was written for use with mapped next generation sequence data but can in theory be used for any dataset which can…

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MethPat
Desktop

MethPat

Enables the summarization and visualization of DNA methylation sequencing data…

Enables the summarization and visualization of DNA methylation sequencing data in the context of epiallelic information. MethPatis a program that processes bisulfite sequencing data following Bismark…

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chroGPS
Desktop

chroGPS

Allows users to integrate and visualize the associations between epigenetic…

Allows users to integrate and visualize the associations between epigenetic factors and their relation to functional genetic elements in low-dimensional maps. chroGPS is a dimensionality reduction…

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BigWig/BigBed
Desktop

BigWig/BigBed

Allow the high-performance display of next-generation sequencing experiment…

Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser.

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MochiView
Desktop

MochiView

Java software that integrates browsing of genomic sequences, features, and data…

Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis.

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MethylViewer
Desktop

MethylViewer

Interactive data analysis of bisulphite DNA sequencing to map chromatin…

Interactive data analysis of bisulphite DNA sequencing to map chromatin structure using DNA methyltransferases.

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CpGviewer
Desktop

CpGviewer

Aims to be a simple integrated tool for handling bisulphite sequencing…

Aims to be a simple integrated tool for handling bisulphite sequencing projects. CpGviewer can process plain text sequences or a variety of electropherogram formats, and allows interactive editing of…

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methVisual
Desktop

methVisual

Enables exploratory analysis and intuitive visualization of DNA methylation…

Enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. MethVisual allows the import of DNA methylation sequences, aligns…

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DMEAS
Desktop

DMEAS DNA Methylation Entropy Analysis Software

Analyzes the distribution of DNA methylation patterns for the quantification of…

Analyzes the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. DMEAS supports the analysis of both locus-specific and genome-wide bisulfite sequencing data.…

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TABSAT
Web
Desktop

TABSAT

Analyzes interpret targeted bisulfite sequencing data. TABSAT is composed of…

Analyzes interpret targeted bisulfite sequencing data. TABSAT is composed of several modules for running quality assessment, genomic alignment, methylation calling, CpG filtering, merging of samples…

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BSviewer
Desktop

BSviewer

Allows visualization of bisulfite sequencing data. BSviewer allows users to…

Allows visualization of bisulfite sequencing data. BSviewer allows users to inspect the DNA methylation dynamics at nucleotide level. The software supports both paired-end and single-end sequencing…

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MethTools
Desktop

MethTools

A collection of software tools for the handling and analysis of DNA methylation…

A collection of software tools for the handling and analysis of DNA methylation data generated by the Bisulfite Genomic Sequencing method.

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Methy-Pipe
Desktop

Methy-Pipe

A software tool that not only fulfills the core data analysis requirements…

A software tool that not only fulfills the core data analysis requirements (e.g. sequence alignment, differential methylation analysis, etc.) but also provides useful tools for methylation data…

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WBSA
Desktop
Web

WBSA Web Service for Bisulfite Sequencing Data Analysis

A free web application for analysis of whole-genome bisulfite-sequencing (WGBS)…

A free web application for analysis of whole-genome bisulfite-sequencing (WGBS) and genome-wide reduced representation bisulfite sequencing (RRBS) data. WBSA not only focuses on CpG methylation, but…

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ViewBS
Desktop

ViewBS

Explores and visualizes bisulfite sequencing (BS-seq) data. ViewBS has several…

Explores and visualizes bisulfite sequencing (BS-seq) data. ViewBS has several top level commands which determine the required and optimal arguments. These commands can be divided into two parts:…

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Methylation…
Web

Methylation plotter

A Web tool that allows the visualization of methylation data in a user-friendly…

A Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality.

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SCREW
Desktop

SCREW Single Cell Reproducible Epigenomics Workflow

Performs standard single-cell DNA methylation analyses. SCREW consists in…

Performs standard single-cell DNA methylation analyses. SCREW consists in several Common Workflow Language (CWL)+Dockerised tools, as well as mini and complete templates workflows.

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Methylmapper
Desktop
Web

Methylmapper

Generates cluster plots from the results of high-throughput methylation…

Generates cluster plots from the results of high-throughput methylation analysis through bisulfite sequencing.

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iMethy
Desktop

iMethy

For investigation and visualization of DNA methylation by high-throughput…

For investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

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RRBS-Analyser
Web

RRBS-Analyser

A comprehensive genome-scale DNA methylation analysis server based on RRBS…

A comprehensive genome-scale DNA methylation analysis server based on RRBS data. RRBS-Analyser can assess sequencing quality, generate detailed statistical information, align the bisulfite-treated…

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mPod
Dataset

mPod methylation profiles of DNA

A resource for human genome-wide tissue-specific DNA methylation profiles. mPod…

A resource for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues,…

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Methylyzer
Web

Methylyzer

Represents DNA methylation data obtained from bisulfite genomic sequencing.…

Represents DNA methylation data obtained from bisulfite genomic sequencing. Graphical representation of the data includes the methylation status of single CpG dinucleotides. Mutations (replacements,…

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