GenArk: towards a million UCSC genome browsers
Abstract 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 visualizat...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-10-01
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| Series: | Genome Biology |
| Online Access: | https://doi.org/10.1186/s13059-023-03057-x |
| _version_ | 1797452450193473536 |
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| author | Hiram Clawson Brian T. Lee Brian J. Raney Galt P. Barber Jonathan Casper Mark Diekhans Clay Fischer Jairo Navarro Gonzalez Angie S. Hinrichs Christopher M. Lee Luis R. Nassar Gerardo Perez Brittney Wick Daniel Schmelter Matthew L. Speir Joel Armstrong Ann S. Zweig Robert M. Kuhn Bogdan M. Kirilenko Michael Hiller David Haussler W. James Kent Maximilian Haeussler |
| author_facet | Hiram Clawson Brian T. Lee Brian J. Raney Galt P. Barber Jonathan Casper Mark Diekhans Clay Fischer Jairo Navarro Gonzalez Angie S. Hinrichs Christopher M. Lee Luis R. Nassar Gerardo Perez Brittney Wick Daniel Schmelter Matthew L. Speir Joel Armstrong Ann S. Zweig Robert M. Kuhn Bogdan M. Kirilenko Michael Hiller David Haussler W. James Kent Maximilian Haeussler |
| author_sort | Hiram Clawson |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-09T15:08:57Z |
| format | Article |
| id | doaj.art-8226e568dade4fd09eb95b95cb4952fa |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-09T15:08:57Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-8226e568dade4fd09eb95b95cb4952fa2023-11-26T13:29:20ZengBMCGenome Biology1474-760X2023-10-012411810.1186/s13059-023-03057-xGenArk: towards a million UCSC genome browsersHiram Clawson0Brian T. Lee1Brian J. Raney2Galt P. Barber3Jonathan Casper4Mark Diekhans5Clay Fischer6Jairo Navarro Gonzalez7Angie S. Hinrichs8Christopher M. Lee9Luis R. Nassar10Gerardo Perez11Brittney Wick12Daniel Schmelter13Matthew L. Speir14Joel Armstrong15Ann S. Zweig16Robert M. Kuhn17Bogdan M. Kirilenko18Michael Hiller19David Haussler20W. James Kent21Maximilian Haeussler22Genomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaLOEWE Centre for Translational Biodiversity GenomicsLOEWE Centre for Translational Biodiversity GenomicsGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaGenomics Institute, University of CaliforniaAbstract 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.https://doi.org/10.1186/s13059-023-03057-x |
| spellingShingle | Hiram Clawson Brian T. Lee Brian J. Raney Galt P. Barber Jonathan Casper Mark Diekhans Clay Fischer Jairo Navarro Gonzalez Angie S. Hinrichs Christopher M. Lee Luis R. Nassar Gerardo Perez Brittney Wick Daniel Schmelter Matthew L. Speir Joel Armstrong Ann S. Zweig Robert M. Kuhn Bogdan M. Kirilenko Michael Hiller David Haussler W. James Kent Maximilian Haeussler GenArk: towards a million UCSC genome browsers Genome Biology |
| 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 |
| url | https://doi.org/10.1186/s13059-023-03057-x |
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