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GenArk: towards a million UCSC genome browsers
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of an...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
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BioMed Central
2023
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| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10544498/ https://www.ncbi.nlm.nih.gov/pubmed/37784172 http://dx.doi.org/10.1186/s13059-023-03057-x |
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| author | Clawson, Hiram Lee, Brian T. Raney, Brian J. Barber, Galt P. Casper, Jonathan Diekhans, Mark Fischer, Clay Gonzalez, Jairo Navarro Hinrichs, Angie S. Lee, Christopher M. Nassar, Luis R. Perez, Gerardo Wick, Brittney Schmelter, Daniel Speir, Matthew L. Armstrong, Joel Zweig, Ann S. Kuhn, Robert M. Kirilenko, Bogdan M. Hiller, Michael Haussler, David Kent, W. James Haeussler, Maximilian |
| author_facet | Clawson, Hiram Lee, Brian T. Raney, Brian J. Barber, Galt P. Casper, Jonathan Diekhans, Mark Fischer, Clay Gonzalez, Jairo Navarro Hinrichs, Angie S. Lee, Christopher M. Nassar, Luis R. Perez, Gerardo Wick, Brittney Schmelter, Daniel Speir, Matthew L. Armstrong, Joel Zweig, Ann S. Kuhn, Robert M. Kirilenko, Bogdan M. Hiller, Michael Haussler, David Kent, W. James Haeussler, Maximilian |
| author_sort | Clawson, Hiram |
| collection | PubMed |
| description | Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies. Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03057-x. |
| format | Online Article Text |
| id | pubmed-10544498 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2023 |
| publisher | BioMed Central |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-105444982023-10-03 GenArk: towards a million UCSC genome browsers Clawson, Hiram Lee, Brian T. Raney, Brian J. Barber, Galt P. Casper, Jonathan Diekhans, Mark Fischer, Clay Gonzalez, Jairo Navarro Hinrichs, Angie S. Lee, Christopher M. Nassar, Luis R. Perez, Gerardo Wick, Brittney Schmelter, Daniel Speir, Matthew L. Armstrong, Joel Zweig, Ann S. Kuhn, Robert M. Kirilenko, Bogdan M. Hiller, Michael Haussler, David Kent, W. James Haeussler, Maximilian Genome Biol Short Report Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies. Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03057-x. BioMed Central 2023-10-02 /pmc/articles/PMC10544498/ /pubmed/37784172 http://dx.doi.org/10.1186/s13059-023-03057-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This 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 | Short Report Clawson, Hiram Lee, Brian T. Raney, Brian J. Barber, Galt P. Casper, Jonathan Diekhans, Mark Fischer, Clay Gonzalez, Jairo Navarro Hinrichs, Angie S. Lee, Christopher M. Nassar, Luis R. Perez, Gerardo Wick, Brittney Schmelter, Daniel Speir, Matthew L. Armstrong, Joel Zweig, Ann S. Kuhn, Robert M. Kirilenko, Bogdan M. Hiller, Michael Haussler, David Kent, W. James Haeussler, Maximilian GenArk: towards a million UCSC genome browsers |
| title | GenArk: towards a million UCSC genome browsers |
| title_full | GenArk: towards a million UCSC genome browsers |
| title_fullStr | GenArk: towards a million UCSC genome browsers |
| title_full_unstemmed | GenArk: towards a million UCSC genome browsers |
| title_short | GenArk: towards a million UCSC genome browsers |
| title_sort | genark: towards a million ucsc genome browsers |
| topic | Short Report |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10544498/ https://www.ncbi.nlm.nih.gov/pubmed/37784172 http://dx.doi.org/10.1186/s13059-023-03057-x |
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