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. 2019 May 1;8(5):giz051.
doi: 10.1093/gigascience/giz051.

Gigwa v2-Extended and improved genotype investigator

Guilhem Sempéré  1   2   3 , Adrien Pétel  2   4 , Mathieu Rouard  2   5 , Julien Frouin  6   7 , Yann Hueber  2   5 , Fabien De Bellis  6   7 , Pierre Larmande  2   4
Affiliations

Gigwa v2-Extended and improved genotype investigator

Guilhem Sempéré et al. Gigascience. .

Abstract

Background: The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution.

Results: Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data).

Conclusions: This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community.

Keywords: BrAPI; GA4GH; HapMap; MongoDB; NoSQL; PLINK; REST; SNP; VCF; genomic variations; indel; interoperability; web.

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Figures

Figure 1:
Figure 1:
High-level diagram of Gigwa architecture and features.
Figure 2:
Figure 2:
Benchmark results.
Figure 3:
Figure 3:
Discriminating variants. A, Filtering parameters and variant distribution. B, A discriminated variant's genotype with complementary information (males in blue, females in yellow). C, Chromosome region as reported by Feulner et al. [27] showing the strongest association with sex determination.
See this image and copyright information in PMC

References

    1. Wang W, Mauleon R, Hu Z, et al. .. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557:43–9. - PMC - PubMed
    1. Alonso-Blanco C, Andrade J, Becker C, et al. .. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell. 2016;166:481–91. - PMC - PubMed
    1. Alexandrov N, Tai S, Wang W, et al. .. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res. 2015;63:2–6. - PMC - PubMed
    1. Danecek P, Auton A, Abecasis G, et al. .. The variant call format and VCFtools. Bioinformatics. 2011;27:2156–8. - PMC - PubMed
    1. Slifer SH. PLINK: key functions for data analysis. Curr Protoc Hum Genet. 2018;97:e59. - PubMed

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