HPG-Msuite, the methylation analysis ultimate tools suite

HPG-Msuite is a powerful and friendly tool kit for DNA methylation analysis and DMR detection.

This suite contains tools that help you in all the steps of the process:

• HPG-Methyl, is an ultrafast and highly sensitive tool for alignment and methylation analysis of Next-Generation Sequencing samples. It works with both single-end and paired-end .fastq files, and it yields the alignment and methylation status of the sample dataset in the form of .bam files
• HPG-Hmapper is a parallel software tool for analyzing DNA hydroximethylation data. It takes .bam files as input data (yielded by HPG-Methyl, Bismark or any other aligner which yields output data with the same format), and it provides a .csv file containing the methylation map for each chromosome. For each position in the chromosome, this tool yields the number of Cs, noCs, 5mCs and 5hmCs aligned by the alignment tool
• HPG-Dhunter is the last step in the methylation analysis. It is a real-time visualization tool based on CUDA, which can analyze the .csv files coming from different DNA samples and detect Differentially Methylated Regions (DMRs) between samples.
• HPG-Dhunter also has a version to automatically identify all the DMRs in all the chromosomes of the genome among all the existing samples. This version is called HPG-Dhunter-Batch. Although this version does not allow visualization, it yields a list of all the DMRs found. The user can then use HPG-Dhunter to inspect the desired DMRs.

Although we highly recommend the use of the HPG-Msuite for DNA methylation analysis and DMR identification, any of the tools included in this suite can be used separately.

How to install the tools in this suite

The most appropriate way of installing the HPG-Msuite is to follow the next steps:

• Install HPG-Methyl into your system
• Install HPG-Hmapper into your system
• Install HPG-Msuite into your system

At this point, it is possible to do the first two steps in DNA methylation analysis: Alignment of the FASTQ files and mapping the BAM files into a CSV file for each chromosome. So, a bunch of files, ordered by sample, chromosome and strand are obtained.

If your computer includes an NVidia device with a Kepler (or later) microarchitecture or a computing capability (version) 3.5 or higher, then it is possible to quickly identify DMRs:

• Make sure that CUDA SDK is installed in your system: open a terminal (Ctrl + Alt + t) and type "nvcc --version". If nothing appears, then a previous CUDA installation is needed (see https://developer.nvidia.com/cuda-downloads and here).
• Install HPG-Dhunter into your system
• Install HPG-Dhunter-Batch into your system

At this point, you can enjoy the full capabilities of HPG-Msuite.