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Quality control software tools | Bisulfite sequencing data analysis

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…
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Pyrotools
Desktop

Pyrotools

Represents the consensus sequences in a region of interest (ROI). Pyrotools is…

Represents the consensus sequences in a region of interest (ROI). Pyrotools is based on the graph technique that resembles the partial order graph or variant graph. It can model error patterns in the…

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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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COHCAP
Desktop

COHCAP City of Hope CpG Island Analysis Pipeline

Provides tools for analysing single-nucleotide resolution methylation data.…

Provides tools for analysing single-nucleotide resolution methylation data. COHCAP is a pipeline that covers most user needs for differential methylation and integration with gene expression 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

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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TABSAT
Web
Desktop

TABSAT

Analyzes interpret targeted bisulfite sequencing data. TABSAT is composed of…

Analyzes interpret targeted bisulfite sequencing data. TABSAT is composed of several modules for running quality assessment, genomic alignment, methylation calling, CpG filtering, merging of samples…

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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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