A computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe is a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.
A probabilistic model to infer allele-specific DNA methylation (ASM) based on data from high-throughput BS-seq experiments. This model is independent of genotype, and therefore has broad applicability to identify ASM in the context of imprinting. In essence, this model describes the degree to which methylation states in reads appear to reflect two distinct patterns, each pattern representing roughly half the data. This method only requires formatted mapped reads (Epiread format) as input, and reports all possible regions of ASM in the genome. amrfinder is a part of the MethPipe Package. Please see the MethPipe homepage for installation details.
Allows to extract multiple types of information (such as DMCs, DMRs, SNPs and ASM) from various types of RRBS and Bis-seq data. SMAP is designed to be an easy-to-use, one-stop and sophisticated package for methylation analyses. The pipeline consists of seven operational stages: (i) reference preparation, (ii) read preparation, (iii) alignment, (iv) calculation of methylation rate, (v) differentially methylated regions (DMR) detection, (vi) single nucleotide polymorphism (SNP) and allele-specific DNA methylation (ASM) calling and (vii) summarization.
Allows user-friendly data exploration, visualization and interpretation of allelic imbalance. MEA furnishes integrated allele-specific analysis of DNA methylation, histone modification and expression data. This software automates diploid pseudo genome reconstruction, allele-specific read detection and haplotype-resolved. It can be used without needing extensive bioinformatic expertise and be installed into a Docker container.