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.
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 high-throughput sequencing data, such as RNA-Seq or ChIP-seq, to elucidate the role of methylated intergenic regions in gene regulation. In essence, GBSA allows an investigator to explore not only known loci but also all the genomic regions, for which methylation studies could lead to the discovery of new regulatory mechanisms.
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.
A fragment-based approach for investigating DNA methylation patterns for reduced representation bisulphite sequencing data. DMAP can directly import the output from any bisulphite aligner in sequence alignment/map (SAM) format and identify differential methylation.
Integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. SAAP-RRBS facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation.
Enables users to associate numerical or categorical data with regions. annotatr is a package that reports all intersections of genomic regions with built-in genomic annotations for D. melanogaster, H. Sapiens, M. musculus, R. norvegicus, annotations imported from the AnnotationHub R package or custom annotations for any organism. It also enables better understanding of the underlying experiments via summarization and visualization functions.
Analyzes whole genome bisulfite sequencing (WGBS) data. bicycle is a next-generation sequencing (NGS) bioinformatic pipeline that can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols and from single-end and paired-end sequencing. It also performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH). It provides statistical methylcytosine calling and offers several filters to screen reads.
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.
Classifies bisulfite-sequencing data. Bis-Class deduces methylation status in the framework of Bayesian probabilistic models to reduce classification errors in the presence of a known alternative hypothesis. It is able to take into account the prior methylation distribution to work. This tool returns biological consistent and relevant information. It is useful for analyses of sparsely methylated genomes such as insect genomes.
Serves for the analysis of whole genome bisulfite sequencing (WGBS) data and for calling methylation for all cytosines in the genome. METHimpute is built on a Hidden Markov Model (HMM) imputation-based imputation algorithm for the construction of complete methylomes from shallow or deep WGBS data. This program can assign the methylation status of cytosines with missing or uninformative coverage and their recalibrated methylation levels.
A software tool that not only fulfills the core data analysis requirements (e.g. sequence alignment, differential methylation analysis, etc.) but also provides useful tools for methylation data annotation and visualization. Specifically, Methy-Pipe uses Burrow-Wheeler Transform (BWT) algorithm to directly align bisulfite sequencing reads to a reference genome and implements a novel sliding window based approach with statistical methods for the identification of differentially methylated regions (DMRs). The capability of processing data parallelly allows it to outperform a number of other bisulfite alignment software packages.
A free web application for analysis of whole-genome bisulfite-sequencing (WGBS) and genome-wide reduced representation bisulfite sequencing (RRBS) data. WBSA not only focuses on CpG methylation, but also allows CHG and CHH analysis. BWA is incorporated as its mapping software. WBSA can be applied to DNA methylation researches for animals and plants and it provides advanced analysis for both WGBS and RRBS. It can also identify differently methylated regions (DMRs) in different strings. WBSA includes six modules: Home, WGBS, RRBS, DMR, Documents and Downloads, and provides the executable package for downloads and local installation. WGBS and RRBS modules include four main steps: pre-processing of reads and reference, alignment to the reference, identification of methylcytosines and annotation. DMR module includes DMRs identification and annotation of the correlative genes.
Allows submission of a list of genomic regions and displaying of the corresponding annotations in a web page. AnnotateGenomicRegions annotates sets of genomic regions of interest with overlapping and/or neighboring features that are mapped to the genome. Moreover, genomic regions of interest can be derived from experiments such as ChIP-seq, DNase hypersensitive sites sequencing (DNase-seq), methylation profiling using reduced representation bisulfite sequencing (Methyl RRBS), quantitation of small RNAs by massively parallel sequencing (Small RNA-seq), resequencing, and more.
An efficient, specialized and highly automated mapping and annotation tool for RNA bisulfite sequencing data. Focusing on both CG and non-CG methylation, BS-RNA can handle the mapping and annotation of either single- or paired-end sequencing reads of directional bisulfite libraries. This tool provide more comprehensive annotation information such as the distribution of cytosine methylation in both gene and transcript levels.
Investigates bisulfite sequencing data. BAT is composed of four main modules: (i) Mapping, that includes utilities for conversion and statistics; (ii) Calling, provides features dedicated to the recovering and filtering of information related to methylation; (iii) Analysis allows users to investigate and annotate several samples and (iv) DMRs, to call and correlate differentially methylated region (DMR).
Detects DNA modifications from single molecule. Kineticstools can be used in real-time sequencing data. It makes independent comparison of IPDs at each position on the genome, for each strand, and emits various statistics. The tool provides results in a variety of formats suitable for in-depth statistical analysis, quick reference, and consumption by visualization tools.
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 epiG depends on a number of user-adjustable parameters. These parameters control how noise is treated and how reads are clustered together to form haplotype chains. epiG starts by assigning each read to its own haplotype chain and then, iteratively, it improves the haplotype chains by re-assigning reads to chains one at a time, using an optimization procedure and prior genetic information.
A comprehensive genome-scale DNA methylation analysis server based on RRBS data. RRBS-Analyser can assess sequencing quality, generate detailed statistical information, align the bisulfite-treated short reads to reference genome, identify and annotate the methylcytosines (5mCs) and associate them with different genomic features in CG, CHG, and CHH content. RRBS-Analyser supports detection, annotation, and visualization of differentially methylated regions (DMRs) for multiple samples from nine reference organisms. Moreover, RRBS-Analyser provides researchers with detailed annotation of DMR-containing genes, which will greatly aid subsequent studies. The input of RRBS-Analyser can be raw FASTQ reads, generic SAM format, or self-defined format containing individual 5mC sites. RRBS-Analyser can be widely used by researchers wanting to unravel the complexities of DNA methylome in the epigenetic community.
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