Bisulfite sequencing data analysis bioinformatics software tools

DNA methylation contributes to the epigenetic regulation of many key developmental processes including genomic imprinting, X-inactivation, genome stability and gene regulation. Bisulfite conversion of genomic DNA combined with next-generation sequencing (BS-seq) is widely used…

BS-seq analysis steps

BS-seq analysis workflow

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BS-seq analysis workflow schema

Most recent bioinformatics tools

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Bscall
Desktop

Bscall

Provides a method for bisulfite sequencing data. Bscall was developed as a…

Provides a method for bisulfite sequencing data. Bscall was developed as a variant caller.

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GEMBS
Desktop

GEMBS

Provides a bioinformatics pipeline specifically designed for the analysis of…

Provides a bioinformatics pipeline specifically designed for the analysis of large whole genome bisulfite sequencing (WGBS) data sets. GEMBS is based on two core modules: (i) GEM3, a high performance…

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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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dmrseq
Desktop

dmrseq

Detects candidate regions and evaluates statistical significance at the region…

Detects candidate regions and evaluates statistical significance at the region level. dmrseq is a two-stage approach that calculates a statistic for each candidate differentially methylated region…

Most popular analytical software

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methyLiftover
Desktop

methyLiftover

A method to map DNA methylation data from bisulfite sequencing approaches to…

A method to map DNA methylation data from bisulfite sequencing approaches to CpG sites measured with the widely used Illumina methylation bead-array platforms. Correlations and median absolute…

CGmapTools
Desktop

CGmapTools

Provides a standard for bisulfite sequencing data related manipulation.…

Provides a standard for bisulfite sequencing data related manipulation. CGmapTools is a command-line bisulfite sequencing analysis toolkit with enhanced features on single-nucleotide variant (SNV)…

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Bismark
Desktop

Bismark

A software package to map and determine the methylation state of BS-Seq reads.…

A software package to map and determine the methylation state of BS-Seq reads. Bismark is easy to use, very flexible and is the first published BS-Seq aligner to seamlessly handle single- and…

BS Seeker
Desktop

BS Seeker

Allows to map the bisulfite-treated short reads. BS Seeker is a bisulfite…

Allows to map the bisulfite-treated short reads. BS Seeker is a bisulfite sequencing (BS) alignment tool that performs genome indexing, read alignment and DNA methylation levels calling for each…

Curators for BS-seq analysis

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