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.
A package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing. At an average 30× genomic coverage, Bis-SNP correctly identified 96% of SNPs using the default high-stringency settings.
A computational tool to accurately identify footprints from bisulfite-sequencing data. MethylSeekR incorporates several methodological improvements and extensions that make it robust and generally applicable. The method is based on a cutoff approach that identifies hypomethylated regions as stretches of consecutive CpGs with methylation levels below a fixed threshold. To achieve high accuracy and sensitivity, MethylSeekR incorporates important preprocessing and filtering steps, and controls segmentation parameters via false discovery rate (FDR) calculations. MethylSeekR is an easy-to-use package that describes in detail each step of the analysis and produces several control plots to facilitate the interpretation of the results and to avoid potential pitfalls in the analysis.
Analyzes the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. DMEAS supports the analysis of both locus-specific and genome-wide bisulfite sequencing data. It progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It determines the DNA methylation level and calculates methylation entropy for genomic segments to enable the quantitative assessment of DNA methylation variations observed in cell populations.