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...

Descripción completa

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
_version_ 1784584642874048512
author Liang, Qihua
Lonardi, Stefano
author_facet Liang, Qihua
Lonardi, Stefano
author_sort Liang, Qihua
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8520301
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-85203012021-10-20 Reference-agnostic representation and visualization of pan-genomes Liang, Qihua Lonardi, Stefano BMC Bioinformatics Software 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. BioMed Central 2021-10-16 /pmc/articles/PMC8520301/ /pubmed/34656081 http://dx.doi.org/10.1186/s12859-021-04424-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Liang, Qihua
Lonardi, Stefano
Reference-agnostic representation and visualization of pan-genomes
title Reference-agnostic representation and visualization of pan-genomes
title_full Reference-agnostic representation and visualization of pan-genomes
title_fullStr Reference-agnostic representation and visualization of pan-genomes
title_full_unstemmed Reference-agnostic representation and visualization of pan-genomes
title_short Reference-agnostic representation and visualization of pan-genomes
title_sort reference-agnostic representation and visualization of pan-genomes
topic Software
url 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
work_keys_str_mv AT liangqihua referenceagnosticrepresentationandvisualizationofpangenomes
AT lonardistefano referenceagnosticrepresentationandvisualizationofpangenomes

Ejemplares similares