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SMAP / Streamlined Methylation Analysis Pipeline

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.

amrfinder

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.