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…
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).
Infers epiallelic haplotypes, annotated with CpG methylation marks and…
Infers epiallelic haplotypes, annotated with CpG methylation marks and polymorphisms, from whole genome bisulphite sequencing data, and nucleosome occupancy from NOMe-seq data. The performance of…
Allows to simultaneously account for both the over-dispersed, count-based…
Allows to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. MACAU is a binomial mixed model and an…
Identifies differentially methylated cytosines and regions. Hidden Markov model…
Identifies differentially methylated cytosines and regions. Hidden Markov model (HMM)-Fisher is efficient and robust in identifying heterogeneous differentially methylated (DM) regions. This method…
Detects differentially methylated (DM) regions from bisulfite sequencing (BS)…
Detects differentially methylated (DM) regions from bisulfite sequencing (BS) data generated from different protocols, such as whole-genome bisulfite sequencing (WGBS) and reduced representative BS.…
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…
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…
An open-source software tool capable of analysing whole-genome bisulfite…
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…