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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…

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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…

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RUbioSeq
Desktop

RUbioSeq

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq…

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq is a multi-platform application that uses well established tools to implement pipelines for DNA-seq, CNAseq,…

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bsseq
Desktop

bsseq

Allows analysis, management and storage of bisulfite sequencing (BS-seq data).…

Allows analysis, management and storage of bisulfite sequencing (BS-seq data). bsseq is the implementation of the BSmooth algorithm 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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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…

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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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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…

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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…

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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…

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SMAP
Desktop

SMAP Streamlined Methylation Analysis Pipeline

Allows to extract multiple types of information (such as DMCs, DMRs, SNPs and…

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…

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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…

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GEMBS
Desktop

GEMBS

Provides a bioinformatics pipeline specifically designed for the analysis of…

Provides a bioinformatics pipeline specifically designed for the analysis of large whole genome bisulfite sequencing (WGBS) data sets. GEMBS is based on two core modules: (i) GEM3, a high performance…

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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…

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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…

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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.

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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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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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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,…

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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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