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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.

Source text:
(Lin et al., 2013) BSeQC: quality control of bisulfite sequencing experiments. Bioinformatics.

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COHCAP / City of Hope CpG Island Analysis Pipeline
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.
SMAP / Streamlined Methylation Analysis Pipeline
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 package for methylation analyses. The pipeline consists of seven operational stages: (i) reference preparation, (ii) read preparation, (iii) alignment, (iv) calculation of methylation rate, (v) differentially methylated regions (DMR) detection, (vi) single nucleotide polymorphism (SNP) and allele-specific DNA methylation (ASM) calling and (vii) summarization.
WBSA / Web Service for Bisulfite Sequencing Data Analysis
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.
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