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Title: Reference-agnostic representation and visualization of pan-genomes
Abstract 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.


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.


The PGV software can be installed via conda or downloaded from The companion PGV browser athttp://pgv.cs.ucr.educan be tested using example bed tracks available from the GitHub page.

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Publisher / Repository:
Springer Science + Business Media
Date Published:
Journal Name:
BMC Bioinformatics
Medium: X
Sponsoring Org:
National Science Foundation
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