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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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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. |
format | Online Article Text |
id | pubmed-8652104 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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