Galaxy tool visualization of NGS data on Hilbert Curve.
What does it do? This tool maps genomic data stored in .bed or .bedgraph files on a Hilbert space-filling curve and creates an image file with visualization of the process. Mapping algorithm provides a method to transfer between one-dimensional and two-dimensional space with preservation of locality. Taking that into account this tool allows the user to:
- inspect distribution of score throughout the whole genome,
- compare distribution of score between up to three datasets,
- easily inspect the quality of data.
The interface for this tool contains several options:
- File with chromosome sizes - Choose a .tsv file from history containing chromosomes sizes. Order of chromosomes in the file will be taken into account during visualization.
- Input files - Choose .bed or .bedgraph file from history to be visualized. You can specify a color to plot dataset with and the threshold above which regions are colored. When specified, regions with a score below the chosen threshold will be ignored during visualization. Use Insert Input Files option to add up to three datasets with separate colors and/or thresholds.
- Create color map with chromosome territories - If selected, the tool will create a separate .png file with chromosome territories map according to mapping algorithm.
- Create text file with color legend - If selected, the tool will create a separate .txt file with information about colors used to plot datasets with.
- Invert colors - If selected, the tool will generate printing friendly visualization on a white background instead of black. Colors used to plot datasets with also will be inverted. It is recommended to also use create a text file with color legend option to keep track of color changes.
- Order of Hilbert Curve - This value alongside reference chromosome sizes affect visualization precision. Using default value (11) results with creation of image with resolution 2048 x 2048px (2^11 x 2^11px). Every pixel corresponds to 2^11 x 2^11/(whole genome length) base pairs.
Currently package isn't available in the Galaxy Tool Shed. To install tools on individual instances of the Galaxy platform perform following steps:
- clone repository into your Galaxy tools/ directory:
git clone https://github.com/sienkie/hilbert.git
- copy lines below into your tool configuration file tool_conf.xml file located in the config/ directory of the Galaxy installation
<section id='ngsdatavis' name="NGS Data Visualization">
<tool file="hilbert/hilbert.xml" />
</section>
For more information about configuring custom tools please refer to this tutorial.