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Bisulfite sequencing software tools

High-throughput sequencing software tools

BS-seq applications

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BS-seq workflow schema

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 to measure the methylation state of a whole genome, the methylome, at single-base resolution (Lister et al., 2009; Bock et al., 2010; Harris et al., 2010).

Most Recent Tools

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OMIC_12656
Differentially methylated…

GetisDMR

A statistical method to detect differentially methylated regions (DMRs) from whole-genome…

A statistical method to detect differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS) datasets. GetisDMR utilizes the beta-binomial regression model to account for confounding effects, as well as biological and…

new
OMIC_12487
Workflows & pipelines

MethFlow

A virtual machine for DNA methylation profiling, genotyping and differential methylation…

A virtual machine for DNA methylation profiling, genotyping and differential methylation analysis. The virtual machine is based on an extended version of our MethylExtract algorithm, Bismark/Bowtie2 for read alignment and methylKit for differential…

new
OMIC_12460
Read alignment

Wildcard ALignment Tool
WALT

A software tool for mapping whole-genome bisulfite sequencing (WGBS) reads. WALT uses a…

A software tool for mapping whole-genome bisulfite sequencing (WGBS) reads. WALT uses a strategy of hashing periodic spaced seeds, which leads to significant speedup compared with the most efficient methods currently available. Although many…

new
OMIC_12442
Methylation scoring

Aggregate on Intervals
AgIn

A linear-time algorithm that combines the kinetic information for neighboring CpG sites…

A linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ∼30-fold from an inbred strain medaka…

Most Popular Tools

popular
OMIC_00600
Methylation scoring

Genome Bisulfite Sequencing Analyser
GBSA

An open-source software tool capable of analysing whole-genome bisulfite sequencing data…

An open-source software tool capable of analysing whole-genome bisulfite sequencing data with either a gene-centric or gene-independent focus. GBSA’s output can be easily integrated with other high-throughput sequencing data, such as RNA-Seq or…

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