MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs
Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. Such need has been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step...
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-10-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022920300012 |
| _version_ | 1797370156369838080 |
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| author | Katharina Jasmin Hoff |
| author_facet | Katharina Jasmin Hoff |
| author_sort | Katharina Jasmin Hoff |
| collection | DOAJ |
| description | Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. Such need has been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs, which can be hosted on any publicly available web server, allow browsing genomes via UCSC Genome Browser servers. The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available. However, the number of steps for creating a novel Assembly Hub is large. In some cases, the format of input files needs to be adapted, which is a difficult task for scientists without programming background. Here, we describe MakeHub, a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion. The pipeline also allows extending previously created Hubs by additional tracks. MakeHub is freely available for downloading at https://github.com/Gaius-Augustus/MakeHub. Keywords: Genome annotation, Annotation visualization, RNA-seq, Genome browser |
| first_indexed | 2024-03-08T17:58:21Z |
| format | Article |
| id | doaj.art-79cdcedd7e484765a6317cc1ebd102c6 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-08T17:58:21Z |
| publishDate | 2019-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-79cdcedd7e484765a6317cc1ebd102c62024-01-02T03:49:51ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292019-10-01175546549MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly HubsKatharina Jasmin Hoff0University of Greifswald, Institute for Mathematics and Computer Science, 17489 Greifswald, Germany; University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, GermanyNovel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. Such need has been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs, which can be hosted on any publicly available web server, allow browsing genomes via UCSC Genome Browser servers. The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available. However, the number of steps for creating a novel Assembly Hub is large. In some cases, the format of input files needs to be adapted, which is a difficult task for scientists without programming background. Here, we describe MakeHub, a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion. The pipeline also allows extending previously created Hubs by additional tracks. MakeHub is freely available for downloading at https://github.com/Gaius-Augustus/MakeHub. Keywords: Genome annotation, Annotation visualization, RNA-seq, Genome browserhttp://www.sciencedirect.com/science/article/pii/S1672022920300012 |
| spellingShingle | Katharina Jasmin Hoff MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs Genomics, Proteomics & Bioinformatics |
| title | MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs |
| title_full | MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs |
| title_fullStr | MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs |
| title_full_unstemmed | MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs |
| title_short | MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs |
| title_sort | makehub fully automated generation of ucsc genome browser assembly hubs |
| url | http://www.sciencedirect.com/science/article/pii/S1672022920300012 |
| work_keys_str_mv | AT katharinajasminhoff makehubfullyautomatedgenerationofucscgenomebrowserassemblyhubs |