PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Cost-effective whole-genome assembly enables comprehensive pangenome creation with resolved haplotypes.
• Pangenome graphs offer enhanced bioinformatics algorithms for sequence alignment, visualization, and functional genomics.
• Pangenome graphs reconcile diverse sequence and coordinate systems, improving read mapping, variant calling, and genotyping.

Purpose of the Study:

• To develop algorithms for effective layout and visual analysis of pangenome graphs.
• To introduce PG2 (PanGenoGrapher), an open-source, web-based platform for pangenome graph analysis.
• To enhance the utility and accessibility of pangenome graph analysis through advanced visualization techniques.

Main Methods:

• Development of novel algorithms for pangenome graph layout and visualization.
• Implementation of these algorithms into an open-source, web-based platform (PG2).
• Utilizing graphical representations to improve bioinformatics task efficiency.

Main Results:

• Algorithms for effective layout and visual analysis of pangenome graphs were presented.
• An open-source, flexible, and user-friendly web-based platform, PG2 (PanGenoGrapher), was introduced.
• PG2 realizes the developed algorithms for enhanced pangenome graph analysis.

Conclusions:

• Advanced visualization techniques integrated into pangenome graph analysis enhance utility and accessibility.
• The PG2 platform provides an accessible tool for researchers in genomics and bioinformatics.
• Source code and user guides are available on GitHub, with a live demo and video demonstration.