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Reference-agnostic representation and visualization of pan-genomes.
Qihua Liang1, Stefano Lonardi2
1Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA. qlian003@ucr.edu.
BMC Bioinformatics
|October 17, 2021
Summary
This study introduces PGV (pan-genome visualization), a novel method for representing and visualizing species pan-genomes. PGV offers an effective way to explore complex genomic variations using a reference-agnostic approach.
Area of Science:
- Genomics
- Bioinformatics
Background:
- The pan-genome encompasses all genetic and non-coding sequences within a species.
- Understanding pan-genomes is crucial for studying species diversity and evolution.
Purpose of the Study:
- To introduce PGV, a reference-agnostic pan-genome visualization tool.
- To enable intuitive and effective visualization of complex genomic variations.
Main Methods:
- Developed PGV based on the concept of consensus ordering.
- Created an interactive genome browser for pan-genome exploration.
Main Results:
- PGV provides a novel representation for species pan-genomes.
- The PGV genome browser effectively visualizes complex structural genomic variations.
Conclusions:
- PGV software is available for installation via conda or download.
- An interactive PGV browser is accessible online for testing with example data.
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