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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

new
OMIC_12735
Methylation scoring

oxidative bisulfite Maximum Likelihood Estimate
oxBS-MLE

An efficient method based on binomial modeling of paired bisulfite and oxidative…

An efficient method based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that oxBS-MLE outperformed alternative methods in estimate accuracy and…

new
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…

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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