biostudies-literatureLiang QNational Science Foundation502https://www.ebi.ac.uk/biostudies/studies/S-EPMC8520301biostudies-literatureUnknown22(1)<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.BMC bioinformaticsReference-agnostic representation and visualization of pan-genomes.PMC8520301IIS-1814359IOS-1543963Lonardi SLiang QfalseReference-agnostic representation and visualization of pan-genomes.<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.2021-01-01T00:00:00Z2021 Oct2025-04-04T08:34:00.165Z2025-04-04T08:34:00.165ZS-EPMC85203013465608110.1186/s12859-021-04424-w