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SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat

BACKGROUND: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate genomic variations across hundreds or even thousands of samples in the post-genomic era. The management and exploration of these large-scale genomic variation data require programming skills...

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Autores principales: Wang, Wenxi, Wang, Zihao, Li, Xintong, Ni, Zhongfu, Hu, Zhaorong, Xin, Mingming, Peng, Huiru, Yao, Yingyin, Sun, Qixin, Guo, Weilong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274028/
https://www.ncbi.nlm.nih.gov/pubmed/32501478
http://dx.doi.org/10.1093/gigascience/giaa060
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author Wang, Wenxi
Wang, Zihao
Li, Xintong
Ni, Zhongfu
Hu, Zhaorong
Xin, Mingming
Peng, Huiru
Yao, Yingyin
Sun, Qixin
Guo, Weilong
author_facet Wang, Wenxi
Wang, Zihao
Li, Xintong
Ni, Zhongfu
Hu, Zhaorong
Xin, Mingming
Peng, Huiru
Yao, Yingyin
Sun, Qixin
Guo, Weilong
author_sort Wang, Wenxi
collection PubMed
description BACKGROUND: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate genomic variations across hundreds or even thousands of samples in the post-genomic era. The management and exploration of these large-scale genomic variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new genomic variation data in diverse species. RESULTS: Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale genomic variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize genomic variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence variations. CONCLUSIONS: SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/.
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spelling pubmed-72740282020-06-10 SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat Wang, Wenxi Wang, Zihao Li, Xintong Ni, Zhongfu Hu, Zhaorong Xin, Mingming Peng, Huiru Yao, Yingyin Sun, Qixin Guo, Weilong Gigascience Technical Note BACKGROUND: The cost of high-throughput sequencing is rapidly decreasing, allowing researchers to investigate genomic variations across hundreds or even thousands of samples in the post-genomic era. The management and exploration of these large-scale genomic variation data require programming skills. The public genotype querying databases of many species are usually centralized and implemented independently, making them difficult to update with new data over time. Currently, there is a lack of a widely used framework for setting up user-friendly web servers to explore new genomic variation data in diverse species. RESULTS: Here, we present SnpHub, a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale genomic variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize genomic variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence variations. CONCLUSIONS: SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http://guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http://wheat.cau.edu.cn/Wheat_SnpHub_Portal/. Oxford University Press 2020-06-05 /pmc/articles/PMC7274028/ /pubmed/32501478 http://dx.doi.org/10.1093/gigascience/giaa060 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
Wang, Wenxi
Wang, Zihao
Li, Xintong
Ni, Zhongfu
Hu, Zhaorong
Xin, Mingming
Peng, Huiru
Yao, Yingyin
Sun, Qixin
Guo, Weilong
SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
title SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
title_full SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
title_fullStr SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
title_full_unstemmed SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
title_short SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
title_sort snphub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274028/
https://www.ncbi.nlm.nih.gov/pubmed/32501478
http://dx.doi.org/10.1093/gigascience/giaa060
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