If you want to use this suite just now, there is an executable file for Linux x86_64 systems. This compressed file is available at releases page. But, very important, HPG-Methyl and HPG-Hmapper tools must be installed in your system before run this suite.
HPG-Msuite is a powerful and friendly tool kit for DNA methylation analysis and DMR detection. The suite contains tools for 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 which works with both single-end or paired-end .fastq files. It yields the alignment and methylation status of the sample dataset in the form of .bam files. The next analysis step can be done with HPG-Hmapper, a parallel software tool for analyzing DNA hydroximethylation data, which works with the .bam files yielded by HPG-Methyl and 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 HPG-Methyl. The last step in the methylation analysis can be carried out with HPG-Dhunter, a powerful, real-time visualizer tool based on CUDA that 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 within the whole genome and among all the existing samples, 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 the other version to inspect the desired DMRs.
HPG-Msuite shows a user interface (UI) whose design has been developed according with usability good practices. HPG-Msuite offers a quick access to automate all the analysis processes, from alignment of fastq samples to DMR detection and visualization.
This is the main UI:
where:
- Launch HPG-Methyl interface.
- System information
- Launch HPG-Hmapper interface.
- Launch HPG-Dhunter application.
Once the HPG-Methyl interface is running, the alignment process of fastq files can be done for all the samples easily. This interface turns the alignment of several samples into an automated process, instead of repeatedly typing the commands for each of the samples.
This is the main UI:
where:
- Burrows-Wheeler transform index is needed for alignment. Here it can be done
- Select the path to chromosome reference .fa
- Select the path to save de BWT index
- Select the compression ratio
- Select the path where the BWT is.
- Select the fastq files to align.
- Delete the file marked
- Rise the line marked in the list (12)
- Go down the line marked in the list (12)
- Select the path to save the BAM aligned files.
- System information.
- List of the fastq selected to align.
- Select if this is a process with paired files to align.
- Progress bar.
- Button to start the process.
- Button to stop the process.
- Button to exit from the interface and return to HPG-Suite interface.
- Select the paired fastq files to align.
- Some parameters of paired alignment process.
- Some parameters of alignment process.
- Select the HPG-Methyl executable file.
In the same way, the HPG-Hmapper interface allows to carry out the mapping process of bam files for several samples easily.
This is the main UI:
where:
- Select the HPG-Hmapper executable file.
- Select the 5mC bam files.
- Delete the file marked.
- Rise the file marked.
- Go down the file marked.
- List of 5mC bam files to map.
- Select if there are 5hmC paired files.
- Select the 5hmC bam files.
- Select the path to save the csv mapped files
- Selexct the path where the BWT index of the chromosome reference is.
- Progress bar.
- System information.
- Button to start the process.
- Button to stop the process.
- Button to exit from the interface and return to HPG-Suite interface.
- Some parameters of mapping process.
Finally, HPG-Dhunter allows the selection of the resuls caming from different samples and the detection of DMRs in the selected chromosomes. The README.md of the git repository can help to work with this tool once it is launched.
For a correct working of HPG-Msuite, a previous installation of HPG-Methyl, HPG-Hmapper and HPG-Dhunter is needed in the same computer. Also, the path to the HPG-Dhunter executable file must be changed in the line 77 of iface.cpp file.
The HPG-Msuite is a useful interface for methylation analysis with HPG tool kit. Then, the system requirement needs to be, at least, the same for HPG-Methyl and HPG-Hmapper, adding a GPU device for HPG-Dhunter. So HPG-Msuite should work properly in a station with the following set-up:
- A 64 bit Intel CPU compatible with SSE4.2.
- The DNA data for DMR tasks needs as adjacent memory as the number of samples by the length of the largest chromosome to be analized. This parameter has a direct relation with the global memory available of the GPU device. The test was done with 32 MB of RAM.
- The amount of samples that HPG-Dhunter can analize at the same time is directly dependent with the amount of the device memory. Working with a Nvidia GeForce GTX 1080 with 8 GB of GRAM, is possible to analyze and visualize up to six samples of chromosome-21 or up to four chromosome-10 or up to two chromosome-1 at the same time.
- The CUDA compilation is configured to a single device with Nvidia Pascal GPU architecture. So, the devices that will work properly are Titan XP and X models, Tesla P40, P6 and P4 models, Quadro P6000, P5000, P4000 models, GeForce GTX 1080Ti, 1080, 1070Ti, 1070 models, and others easy to find here.
- The Nvidia driver is needed (v384 or higher).
- The CUDA API is needed(v9 or higher).
- For a complete installation of Nvidia drivers and CUDA, it can download just one file from here and follow the instructions, that appear in the same page after select the distribution and version, for a pretty installation.
If you are interested in modifying, extending or debugging the software, the way to build HPG-Msuite in your system is opening the software as a project inside an installed QtCreator (> v4.5, Qt > v5.11, GCC 5) IDE and build it from there.
HPG-Msuite - Copyright (C) 2019 - grev-uv This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions; visit https://www.gnu.org/copyleft/gpl.html for details. However, if you find any bugs, issues, want a specific feature added or need help, feel free to add an issue or extend an existing one. Pull requests are welcome.
HPG-Msuite is free software and licensed under the GNU General Public License version 3. HPG-Msuite was developed under Qt as a platform application development framework for linux/ubuntu desktop, using a free software LGPL v3 license.
Contact any of the following developers for any enquiry:
- Juanma Orduña (juan.orduna@uv.es).
- Mariano Pérez (mariano.perez@uv.es).
- Lisardo Fernández (lisardo.fernandez@uv.es).