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. Source text: Su et al., 2013.

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Bismark
Desktop

Bismark

A software package to map and determine the methylation state of BS-Seq reads.…

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…

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GBSA
Desktop

GBSA Genome Bisulfite Sequencing Analyser

An open-source software tool capable of analysing whole-genome bisulfite…

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…

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methylKit
Desktop

methylKit

An R package for DNA methylation analysis and annotation from high-throughput…

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…

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PASS
Desktop

PASS

Aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying…

Aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands. The output of…

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Bis-SNP
Desktop

Bis-SNP

A package based on the Genome Analysis Toolkit (GATK) map-reduce framework for…

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×…

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CyMATE
Web

CyMATE Cytosine Methylation Analysis Tool for Everyone

A software platform to perform in silico analyses of DNA methylation at…

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…

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MethylSeekR
Desktop

MethylSeekR

A computational tool to accurately identify footprints from…

A computational tool to accurately identify footprints from bisulfite-sequencing data. MethylSeekR incorporates several methodological improvements and extensions that make it robust and generally…

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Bisulfighter
Desktop

Bisulfighter

A software package for detecting methylated cytosines (mCs) and differentially…

A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.

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BS Seeker
Desktop
Web

BS Seeker

Provides fast and accurate mapping of bisulfite-converted reads. BS-Seeker2 is…

Provides fast and accurate mapping of bisulfite-converted reads. BS-Seeker2 is an updated version of BS Seeker, as a full pipeline for mapping bisulfite sequencing data and generating DNA methylomes.…

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BISMA
Desktop

BISMA

The software is designed for the analysis of bisulfite sequencing data which…

The software is designed for the analysis of bisulfite sequencing data which are derived from sequencing of subcloned molecules of a PCR product.

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COHCAP
Desktop

COHCAP City of Hope CpG Island Analysis Pipeline

An algorithm to analyze single-nucleotide resolution methylation data.

An algorithm to analyze single-nucleotide resolution methylation data.

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BatMeth
Desktop

BatMeth

An efficient and accurate general-purpose bisulfite sequence mapping program.…

An efficient and accurate general-purpose bisulfite sequence mapping program. BatMeth can be deployed for the analysis of genome-wide bisulfite sequencing using either base reads or color reads. It…

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MethylCoder
Desktop

MethylCoder

Generates per-base methylation data given a set of bisulfite-treated reads.…

Generates per-base methylation data given a set of bisulfite-treated reads. MethylCoder provides the option to use either of two existing short-read aligners, each with different strengths. It…

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MethPipe
Desktop

MethPipe

A computational pipeline for analyzing bisulfite sequencing data (WGBS and…

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…

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SAAP-RRBS
Desktop

SAAP-RRBS Streamlined Analysis and Annotation Pipeline for RRBS data

Integrates read quality assessment/clean-up, alignment, methylation data…

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…

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MLML
Desktop

MLML

A useful tool to simultaneously estimate hydroxymethylation (5hmC) and…

A useful tool to simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels from BS-seq, oxBS-seq and TAB-seq experiments.

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DMEAS
Desktop

DMEAS DNA Methylation Entropy Analysis Software

Analyzes the distribution of DNA methylation patterns for the quantification of…

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.…

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MethylExtract
Desktop

MethylExtract

A user friendly tool to: i) generate high quality, whole genome methylation…

A user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script…

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MSC
Desktop

MSC Methylation Status Calling

A classification-based procedure to make binary methylation status calls.

A classification-based procedure to make binary methylation status calls.

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FadE
Desktop

FadE

A software package which was designed to determine the methylation parameter at…

A software package which was designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome.

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Bycom
Desktop

Bycom

It can do methylcytosine calling from BS-seq (WGBS and RRBS), and either…

It can do methylcytosine calling from BS-seq (WGBS and RRBS), and either unmapped reads (FASTQ) or mapped reads (SAM/BAM) could be permitted for the input data.

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ampliMethProfil…
Desktop

ampliMethProfiler

Extracts and analyzes the epihaplotype composition of reads from targeted…

Extracts and analyzes the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is a python-based pipeline for the extraction and statistical…

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BRAT-nova
Desktop

BRAT-nova Bisulfite-treated Reads Analysis Tool-nova

A completely rewritten and improved implementation of the mapping tool BRAT-BW…

A completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-seq). BRAT-nova employs a novel space-efficient representation of the genome and…

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NGSmethPipe
Desktop

NGSmethPipe

Generates high-quality methylation maps. NGSmethPipe generates single…

Generates high-quality methylation maps. NGSmethPipe generates single base-pair-resolution methylation maps from bisulfite conversion high throughput sequencing experiments. It processes into 4 steps…

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DMAP
Desktop

DMAP

A fragment-based approach for investigating DNA methylation patterns for…

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…

oxBS-MLE
Desktop

oxBS-MLE oxidative bisulfite Maximum Likelihood Estimate

An efficient method based on binomial modeling of paired bisulfite and…

An efficient method based on binomial modeling of paired bisulfite and oxidative bisulfite data from sequencing or array analysis. Evaluation in several datasets showed that oxBS-MLE outperformed…

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AgIn
Desktop

AgIn Aggregate on Intervals

A linear-time algorithm that combines the kinetic information for neighboring…

A linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read…

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DeepCpG
Desktop

DeepCpG

A computational approach based on deep neural networks to predict DNA…

A computational approach based on deep neural networks to predict DNA methylation states from DNA sequence and incomplete methylation profiles in single cells. We validate DeepCpG on mouse embryonic…

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Lux
Desktop

Lux

A generative model to quantify DNA methylation modifications from any…

A generative model to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and…

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FASTmC
Web

FASTmC

A suite of predictive models for non-reference, cost-effective exploration and…

A suite of predictive models for non-reference, cost-effective exploration and comparative analysis of context-specific DNA methylation levels. Accurate estimations of true DNA methylation levels can…

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SMAP
Desktop

SMAP Streamlined Methylation Analysis Pipeline

A streamlined package to meet the need of extracting multiple types of…

A streamlined package to meet the need of extracting multiple types of information (such as differentially methylated C sites (DMCs), differentially methylated regions (DMRs), single nucleotide…

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segmentSeq
Desktop

segmentSeq

Analyses small RNA sequencing data from multiple biological sources, taking…

Analyses small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. The segmentSeq R package has been extended…

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BSPAT
Desktop
Web

BSPAT Bisulfite Sequencing Pattern Analysis Tool

A fast online service for analysing co-occurrence methylation patterns in…

A fast online service for analysing co-occurrence methylation patterns in bisulfite sequencing data. BSPAT integrated sequence mapping, quality control and visualized analysis result of co-occurrence…

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Methy-Pipe
Desktop

Methy-Pipe

A software tool that not only fulfills the core data analysis requirements…

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…

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MethyQA
Desktop

MethyQA

Provides users with a unique insight into the methylation sequencing data they…

Provides users with a unique insight into the methylation sequencing data they are researching. MethyQA allows the users to determine the quality of their data and better prepares them to address the…

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WBSA
Desktop
Web

WBSA Web Service for Bisulfite Sequencing Data Analysis

A free web application for analysis of whole-genome bisulfite-sequencing (WGBS)…

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…

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BEAT
Desktop

BEAT BS-Seq Epimutation Analysis Toolkit

Delivers methods for the estimation of methylation levels, methylation status…

Delivers methods for the estimation of methylation levels, methylation status and for calling epimutation events in a two-sample comparison. BEAT implements all bioinformatics steps required for the…

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Kismeth
Web

Kismeth

A web-based tool for bisulfite sequencing analysis. Kismeth was designed to be…

A web-based tool for bisulfite sequencing analysis. Kismeth was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It…

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CpG_MPs
Desktop

CpG_MPs

A comprehensive tool for identification and analysis of the methylation…

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…

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RRBS-Analyser
Web

RRBS-Analyser

A comprehensive genome-scale DNA methylation analysis server based on RRBS…

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…

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