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Single nucleotide polymorphism identification software tools | Bisulfite sequencing data analysis

Bisulfite treatment of DNA followed by high-throughput sequencing (Bisulfite-seq) is an important method for studying DNA methylation and epigenetic gene regulation, yet current software tools do not adequately address single nucleotide polymorphisms (SNPs). Identifying SNPs is important for accurate quantification of methylation levels and for identification of allele-specific epigenetic events such as imprinting.

Source text:
(Liu et al., 2012) Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol.

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CGmapTools
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Provides a standard for bisulfite sequencing data related manipulation. CGmapTools is a command-line bisulfite sequencing analysis toolkit with enhanced features on single-nucleotide variant (SNV) calling and allele specific methylations and visualizations. It includes modules for better data storage, extraction, visualization and improved performance in single-nucleotide polymorphism (SNP) calling.
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.
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