Quality assessment 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 suitable for subsequent analysis.
Serves for importation, quality control (QC), analysis, and visualization of methylation data generated using Sequenom's MassArray platform. MassArray is a program able to perform detailed amplicon prediction for optimal assay design. It can also inform researchers about quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Additionally, it can flag potentially confounded data from specific CG sites by using automatic single nucleotide polymorphism (SNP)-detection.
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 DNA methylation patterns. Besides, BSPAT is much faster than existing tools which are based on multiple sequence alignment and pair-wise sequence alignment algorithms.
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 annotated CpG methylation report to biological interpretation.
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 takes standard SAM/BAM files as input and generates bias-free SAM/BAM files for downstream analysis. Evaluation based on real BS-seq data indicates that the use of the bias-free SAM/BAM file substantially improves the quantification of methylation level.
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. The software includes quality control metrics, defining differentially methylated CpG sites, defining differentially methylated CpG islands and visualization of methylation data. It contains two different methods of CpG island analysis. COHCAP has been shown scalable for high-quality integrative analysis of cell line data as well as large heterogeneous patient samples.
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 also allows CHG and CHH analysis. BWA is incorporated as its mapping software. WBSA can be applied to DNA methylation researches for animals and plants and it provides advanced analysis for both WGBS and RRBS. It can also identify differently methylated regions (DMRs) in different strings. WBSA includes six modules: Home, WGBS, RRBS, DMR, Documents and Downloads, and provides the executable package for downloads and local installation. WGBS and RRBS modules include four main steps: pre-processing of reads and reference, alignment to the reference, identification of methylcytosines and annotation. DMR module includes DMRs identification and annotation of the correlative genes.