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Panache: a web browser-based viewer for linearized pangenomes

MOTIVATION: Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficie...

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Detalles Bibliográficos
Autores principales: Durant, Éloi, Sabot, François, Conte, Matthieu, Rouard, Mathieu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8652104/
https://www.ncbi.nlm.nih.gov/pubmed/34601567
http://dx.doi.org/10.1093/bioinformatics/btab688
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author Durant, Éloi
Sabot, François
Conte, Matthieu
Rouard, Mathieu
author_facet Durant, Éloi
Sabot, François
Conte, Matthieu
Rouard, Mathieu
author_sort Durant, Éloi
collection PubMed
description MOTIVATION: Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness. RESULTS: We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective. AVAILABILITY AND IMPLEMENTATION: Panache is available at github.com/SouthGreenPlatform/panache under the MIT License.
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spelling pubmed-86521042021-12-08 Panache: a web browser-based viewer for linearized pangenomes Durant, Éloi Sabot, François Conte, Matthieu Rouard, Mathieu Bioinformatics Applications Notes MOTIVATION: Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness. RESULTS: We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective. AVAILABILITY AND IMPLEMENTATION: Panache is available at github.com/SouthGreenPlatform/panache under the MIT License. Oxford University Press 2021-10-02 /pmc/articles/PMC8652104/ /pubmed/34601567 http://dx.doi.org/10.1093/bioinformatics/btab688 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Durant, Éloi
Sabot, François
Conte, Matthieu
Rouard, Mathieu
Panache: a web browser-based viewer for linearized pangenomes
title Panache: a web browser-based viewer for linearized pangenomes
title_full Panache: a web browser-based viewer for linearized pangenomes
title_fullStr Panache: a web browser-based viewer for linearized pangenomes
title_full_unstemmed Panache: a web browser-based viewer for linearized pangenomes
title_short Panache: a web browser-based viewer for linearized pangenomes
title_sort panache: a web browser-based viewer for linearized pangenomes
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8652104/
https://www.ncbi.nlm.nih.gov/pubmed/34601567
http://dx.doi.org/10.1093/bioinformatics/btab688
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