Reference-agnostic representation and visualization of pan-genomes
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Updated: Oct 16, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Qihua Liang1, Stefano Lonardi2
1Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA. qlian003@ucr.edu.
Background:
The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.
Results:
Here we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.
Conclusions:
The PGV software can be installed via conda or downloaded from https://github.com/ucrbioinfo/PGV . The companion PGV browser at http://pgv.cs.ucr.edu can be tested using example bed tracks available from the GitHub page.
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