Bisulfite sequencing (BS-seq) has emerged as the gold standard to study genome-wide DNA methylation at single-nucleotide resolution. Quality control (QC) is a critical step in the analysis pipeline to ensure that BS-seq data are of high quality and suitable for subsequent…
Desktop app
G T A T C G C T A City of Hope CpG… City of Hope CpG Island Analysis Pipeline

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.

Desktop app
G T A T C G C T A Streamlined Analysis… Streamlined Analysis and Annotation Pipeline for…

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…

Desktop app
G T A T C G C T A BSeQC BSeQC

BSeQC

A package to comprehensively evaluate the quality of BS-seq experiments and…

A package to comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases that may result in inaccurate methylation estimation. BSeQC…

Desktop app
G T A T C G C T A ME-plot ME-plot

ME-plot

Detects the errors in bisulfite sequencing mapping data and produce higher…

Detects the errors in bisulfite sequencing mapping data and produce higher quality methylation calls by trimming low quality portions of the reads. Our simulation results on both randomly generated…

Desktop app
G T A T C G C T A Streamlined… Streamlined Methylation Analysis Pipeline

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…

Desktop app
Web app
G T A T C G C T A Bisulfite Sequencing… Bisulfite Sequencing Pattern Analysis Tool

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…

Desktop app
G T A T C G C T A MethyQA MethyQA

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…

Desktop app
Web app
G T A T C G C T A Web Service for… Web Service for Bisulfite Sequencing Data Analysis

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…

Desktop app
G T A T C G C T A BSmooth BSmooth

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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