Reference-agnostic representation and visualization of pan-genomes

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 cons...

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Detalles Bibliográficos
Autores principales: Liang, Qihua, Lonardi, Stefano
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8520301/
https://www.ncbi.nlm.nih.gov/pubmed/34656081
http://dx.doi.org/10.1186/s12859-021-04424-w
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04424-w.

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