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…
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Bis-SNP
Desktop

Bis-SNP

A package based on the Genome Analysis Toolkit (GATK) map-reduce framework for…

A package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing. At an average 30×…

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MethylExtract
Desktop

MethylExtract

A user friendly tool to: i) generate high quality, whole genome methylation…

A user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script…

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BS-SNPer
Desktop

BS-SNPer

An ultrafast and memory-efficient package named BS-SNPer for the exploration of…

An ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared to Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times…

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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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