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…
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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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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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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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BSeQC
Desktop

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…

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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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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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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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ME-plot
Desktop

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…

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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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