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Workflow/pipeline software tools | Bisulfite sequencing data analysis

RnBeads
Desktop

RnBeads

An R package for comprehensive analysis of DNA methylation data obtained with…

An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite…

G T A T C G C T A
epiGBS
Desktop

epiGBS

A reduced representation bisulfite sequencing method for cost-effective…

A reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNA methylation and genetic variation in hundreds of samples de novo. epiGBS method…

G T A T C G C T A
BSmooth
Desktop

BSmooth

A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data.

A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data.

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QUMA
Dataset

QUMA QUantification tool for Methylation Analysis

Aligns, visualizes and quantifies easily bisulfite sequence data for CpG…

Aligns, visualizes and quantifies easily bisulfite sequence data for CpG methylation analysis.

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BioVLAB-mCpG-SN…
Web

BioVLAB-mCpG-SNP-EXPRESS

Enables to examine the multi-omics integrated analysis and supplies users a way…

Enables to examine the multi-omics integrated analysis and supplies users a way to study their own multi-omics data. It works on the integrated analysis of gene expression, DNA methylation, and…

G T A T C G C T A
QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

G T A T C G C T A
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…

G T A T C G C T A
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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P3BSseq
Desktop

P3BSseq Parallel Processing Pipeline for analysis of Bisulfite Sequencing data

A pipeline for automatic analysis of Bisulfite sequencing (BSseq) reads that…

A pipeline for automatic analysis of Bisulfite sequencing (BSseq) reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment and generates…

G T A T C G C T A
methylPipe
Desktop

methylPipe

Memory efficient analysis of base resolution DNA methylation data in both the…

Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or…

G T A T C G C T A
MOABS
Desktop

MOABS MOdel based Analysis of Bisulfite Sequencing data

A complete, accurate and efficient solution for analysis of large scale…

A complete, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing. MOABS seamlessly integrates…

G T A T C G C T A
RUbioSeq
Desktop

RUbioSeq

Facilitates the primary and secondary analysis of re-sequencing projects by…

Facilitates the primary and secondary analysis of re-sequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (single-nucleotide variants and…

G T A T C G C T A
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…

G T A T C G C T A
GobyWeb
Web

GobyWeb

A web application to aid with the analysis of high-throughput sequencing data.…

A web application to aid with the analysis of high-throughput sequencing data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of…

G T A T C G C T A
MethGo
Desktop

MethGo

A software tool designed for the analysis of data from whole-genome bisulfite…

A software tool designed for the analysis of data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS). MethGo provides both genomic and epigenomic…

G T A T C G C T A
MethFlow
Desktop

MethFlow

A virtual machine for DNA methylation profiling, genotyping and differential…

A virtual machine for DNA methylation profiling, genotyping and differential methylation analysis. The virtual machine is based on an extended version of our MethylExtract algorithm, Bismark/Bowtie2…

G T A T C G C T A
methylSig
Desktop

methylSig

R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced…

R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments.

G T A T C G C T A
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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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…

G T A T C G C T A
Strand NGS
Desktop

Strand NGS

An integrated platform that provides analysis, management and visualization…

An integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq,…

G T A T C G C T A
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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