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. 2016 Jun 6:5:25.
doi: 10.1186/s13742-016-0131-8.

Gigwa-Genotype investigator for genome-wide analyses

Guilhem Sempéré  1   2 , Florian Philippe  3 , Alexis Dereeper  4   5 , Manuel Ruiz  4   6   7   8 , Gautier Sarah  4   9 , Pierre Larmande  4   3   7   10
Affiliations

Gigwa-Genotype investigator for genome-wide analyses

Guilhem Sempéré et al. Gigascience. .

Erratum in

Abstract

Background: Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions.

Description: Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats.

Conclusions: The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.

Keywords: Genomic variations; HapMap; INDEL; MongoDB; NoSQL; SNP; VCF; Web interface.

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Figures

Fig. 1
Fig. 1
Action panel enabling project selection, progress indication, abort and export functionalities
Fig. 2
Fig. 2
Variant-filtering interface, allowing search criteria definition and result browsing
Fig 3
Fig 3
Variant detail dialogue, providing variant metadata and genotype-level information
Fig. 4
Fig. 4
Response-time plot by tool for first benchmarked query (location-based filter). VCFtools is by far the slowest option
Fig. 5
Fig. 5
Response-time plot by tool for second benchmarked query (MAF filter). MySQL is by far the slowest option
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References

    1. Gheyas A, Boschiero C, Eory L, Ralph H, Kuo R, Woolliams J, et al. Functional classification of 15 million SNPs detected from diverse chicken populations. DNA Res. 2015;22(3):205–17. doi: 10.1093/dnares/dsv005. - DOI - PMC - PubMed
    1. Li X, Buitenhuis AJ, Lund MS, Li C, Sun D, Zhang Q, et al. Joint genome-wide association study for milk fatty acid traits in Chinese and Danish Holstein populations. J Dairy Sci. 2015;98(11):8152–63. doi: 10.3168/jds.2015-9383. - DOI - PubMed
    1. Shinada H, Yamamoto T, Sato H, Yamamoto E, Hori K, Yonemaru J, et al. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping. Breed Sci. 2015;65(5):388–95. doi: 10.1270/jsbbs.65.388. - DOI - PMC - PubMed
    1. Marcotuli I, Houston K, Waugh R, Fincher GB, Burton RA, Blanco A, et al. Genome wide association mapping for arabinoxylan content in a collection of tetraploid wheats. PLoS One. 2015;10(7):e0132787. doi: 10.1371/journal.pone.0132787. - DOI - PMC - PubMed
    1. The 3000 rice genomes project. The 3,000 rice genomes project. Gigascience. 2014; 3:7. http://dx.doi.org/10.1186/2047-217X-3-7

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