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

  1. Wenxi Wang
  2. Zihao Wang
  3. Xintong Li
  4. Zhongfu Ni
  5. Zhaorong Hu
  6. Mingming Xin
  7. Huiru Peng
  8. Yingyin Yao
  9. Qixin Sun
  10. Weilong Guo

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Abstract

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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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giaa060

    Wenxi Wang 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZihao Wang 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteXintong Li 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhongfu Ni 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteZhaorong Hu 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMingming Xin 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuiru Peng 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYingyin Yao 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteQixin Sun 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteWeilong Guo 1Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, ChinaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: guoweilong@cau.edu.cn

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa060 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102267 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102268

  2. Version published to 10.1093/gigascience/giaa060
  3. Version published to 10.1101/626705v2 on bioRxiv
  4. Version published to 10.1101/626705v1 on bioRxiv