This is the Linux app named MethylExtract whose latest release can be downloaded as MethylExtract.tgz. It can be run online in the free hosting provider OnWorks for workstations.
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MethylExtract
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DESCRIPTION
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in SNP and genotype calling based on non-bisulfite treated reads.
Features
- Methylation and SNV calling from NGS BS-Seq experiments
- Detects and removes potential PCR duplicates
- Putative bisulfite failures detection
- Sequencing errors control
- Statistical bisulfite failure assessment
- Bisulfite SAM / BAM files processing
- Multithreading and memory control
Programming Language
Perl
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/methylextract/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
