Methylation scoring software tools | Bisulfite sequencing data analysis
High-throughput bisulfite sequencing is widely used to measure cytosine methylation at single-base resolution in eukaryotes. It permits systems-level analysis of genomic methylation patterns associated with gene expression and chromatin structure.
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 paired-end mapping of both directional and non-directional bisulfite libraries. The output of Bismark is easy to interpret and is intended to be analysed directly by the researcher performing the experiment.
An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. methylKit is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.
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 cytosine. The software was improved utilizing multiple short-read mapping aligners, supporting gapped mapping and local alignment and building special indexes for handling reduced represented bisulfite sequencing (RRBS) data.
A software platform to perform in silico analyses of DNA methylation at cytosine sites. CyMATE is suitable for analyses of sequence data obtained with bisulfite genomic sequencing and hairpin-bisulfite sequencing, i.e. single-strand and double-strand DNA data. A module for mutation analysis at non-methylation sites is also available. It has been designed as a universal tool for quick, comprehensive and automated analysis of bisulfite sequencing data, providing detailed qualitative and quantitative results. Analysis with CyMATE is simple, very fast, platform-independent and the most detailed of computational analysis methods.
Serves for inter-sample and differential methylation analysis of whole genome bisulfite sequencing (WGBS) data. informME takes in consideration all information available in methylation reads, and takes into account statistical dependencies between the methylation states of CpG sites. Moreover, it can quantify methylation stochasticity not by simple means and variances at individual CpG sites but by using joint probability distributions over the methylation states.
A comprehensive tool for identification and analysis of the methylation patterns of genomic regions from bisulfite sequencing data. CpG_MPs first normalizes bisulfite sequencing reads into methylation level of CpGs. Then it identifies unmethylated and methylated regions using the methylation status of neighboring CpGs by hotspot extension algorithm without knowledge of pre-defined regions. Furthermore, the conservatively and differentially methylated regions across paired or multiple samples (cells or tissues) are identified by combining a combinatorial algorithm with Shannon entropy.