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Plant Bioinformatics pp 415–427Cite as

Managing High-Density Genotyping Data with Gigwa

Part of the Methods in Molecular Biology book series (MIMB,volume 2443)

Abstract

Next generation sequencing technologies enabled high-density genotyping for large numbers of samples. Nowadays SNP calling pipelines produce up to millions of such markers, but which need to be filtered in various ways according to the type of analyses. One of the main challenges still lies in the management of an increasing volume of genotyping files that are difficult to handle for many applications. Here, we provide a practical guide for efficiently managing large genomic variation data using Gigwa, a user-friendly, scalable and versatile application that may be deployed either remotely on web servers or on a local machine.

Key words

  • NoSQL database
  • SNP markers
  • INDELs
  • VCF
  • Web tool
  • Interoperability

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Acknowledgments

This work was technically supported by the CIRAD-UMR AGAP and IRD-Itrop HPC Data Centers of the South Green Bioinformatics platform (https://www.southgreen.fr/). The authors would also like to thank Manuel Ruiz for providing the original idea, Valentin Guignon for developing a Gigwa module for Drupal, and the BrAPI community for interactions that helped improve and promote the software.

Author information

Authors and Affiliations

  1. CIRAD, UMR INTERTRYP, Montpellier, France

    Guilhem Sempéré

  2. INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France

    Guilhem Sempéré

  3. French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France

    Guilhem Sempéré, Pierre Larmande & Mathieu Rouard

  4. DIADE, Univ Montpellier, IRD, Montpellier, France

    Pierre Larmande

  5. Bioversity International, Parc Scientifique Agropolis II, Montpellier, France

    Mathieu Rouard

Authors
  1. Guilhem Sempéré
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  2. Pierre Larmande
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  3. Mathieu Rouard
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Corresponding author

Correspondence to Pierre Larmande .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Western Australia, Perth, WA, Australia

    Prof. Dr. David Edwards

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Sempéré, G., Larmande, P., Rouard, M. (2022). Managing High-Density Genotyping Data with Gigwa. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_21

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  • DOI: https://doi.org/10.1007/978-1-0716-2067-0_21

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2066-3

  • Online ISBN: 978-1-0716-2067-0

  • eBook Packages: Springer Protocols

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