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GenoVi, an open-source automated circular genome visualizer for bacteria and archaea
The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104344/ https://www.ncbi.nlm.nih.gov/pubmed/37014908 http://dx.doi.org/10.1371/journal.pcbi.1010998 |
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author | Cumsille, Andrés Durán, Roberto E. Rodríguez-Delherbe, Andrea Saona-Urmeneta, Vicente Cámara, Beatriz Seeger, Michael Araya, Mauricio Jara, Nicolás Buil-Aranda, Carlos |
author_facet | Cumsille, Andrés Durán, Roberto E. Rodríguez-Delherbe, Andrea Saona-Urmeneta, Vicente Cámara, Beatriz Seeger, Michael Araya, Mauricio Jara, Nicolás Buil-Aranda, Carlos |
author_sort | Cumsille, Andrés |
collection | PubMed |
description | The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi’s potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi. |
format | Online Article Text |
id | pubmed-10104344 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-101043442023-04-15 GenoVi, an open-source automated circular genome visualizer for bacteria and archaea Cumsille, Andrés Durán, Roberto E. Rodríguez-Delherbe, Andrea Saona-Urmeneta, Vicente Cámara, Beatriz Seeger, Michael Araya, Mauricio Jara, Nicolás Buil-Aranda, Carlos PLoS Comput Biol Research Article The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi’s potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi. Public Library of Science 2023-04-04 /pmc/articles/PMC10104344/ /pubmed/37014908 http://dx.doi.org/10.1371/journal.pcbi.1010998 Text en © 2023 Cumsille et al 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 use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Cumsille, Andrés Durán, Roberto E. Rodríguez-Delherbe, Andrea Saona-Urmeneta, Vicente Cámara, Beatriz Seeger, Michael Araya, Mauricio Jara, Nicolás Buil-Aranda, Carlos GenoVi, an open-source automated circular genome visualizer for bacteria and archaea |
title | GenoVi, an open-source automated circular genome visualizer for bacteria and archaea |
title_full | GenoVi, an open-source automated circular genome visualizer for bacteria and archaea |
title_fullStr | GenoVi, an open-source automated circular genome visualizer for bacteria and archaea |
title_full_unstemmed | GenoVi, an open-source automated circular genome visualizer for bacteria and archaea |
title_short | GenoVi, an open-source automated circular genome visualizer for bacteria and archaea |
title_sort | genovi, an open-source automated circular genome visualizer for bacteria and archaea |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104344/ https://www.ncbi.nlm.nih.gov/pubmed/37014908 http://dx.doi.org/10.1371/journal.pcbi.1010998 |
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