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Metagenomics Bioinformatic Pipeline

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Plant Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2512))

Abstract

Microbial communities’ taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment. Nevertheless, the programming skills needed and the amount of software available may be overwhelming to someone trying to analyze these data. Here, we present a comprehensive and straightforward pipeline that takes shotgun metagenomics data through the needed steps to obtain valuable results. The raw data goes through a quality control process, metagenomic assembly, binning (the obtention of single genomes from a metagenome), taxonomic assignment, and taxonomic diversity analysis and visualization.

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Acknowledgments

The authors would like to thank all the learners, helpers, and instructors who gave feedback on the consolidation of this pipeline. To Ahmed Moustafa for his advice and support in the writing of this chapter. Finally, we thank the Mexican population, which supports the training of scientists within the country. The research reported in this publication was supported by CONACyT “MicroAgrobioma” grant 320237.

Author information

Authors and Affiliations

  1. Laboratorio de Genómica Ecológica y Evolutiva, Langebio, Cinvestav, Mexico

    Diego Garfias-Gallegos & Claudia Zirión-Martínez

  2. Laboratorio de Evolución de la Diversidad Metabólica, Langebio, Cinvestav, Mexico

    Edder D. Bustos-Díaz

  3. Laboratorio de Sistemas Genéticos, Langebio, Cinvestav, Mexico

    Tania Vanessa Arellano-Fernández & J. Abraham Avelar-Rivas

  4. Escuela Nacional de Estudios Superiores, Unidad León, UNAM, León, Mexico

    Tania Vanessa Arellano-Fernández, José Abel Lovaco-Flores & Aarón Espinosa-Jaime

  5. BetterLab—C3, Irapuato, Mexico

    José Abel Lovaco-Flores & Nelly Sélem-Mójica

  6. Centro de Ciencias Matemáticas, UNAM, Morelia, Mexico

    Nelly Sélem-Mójica

Authors
  1. Diego Garfias-Gallegos
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  2. Claudia Zirión-Martínez
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  3. Edder D. Bustos-Díaz
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  4. Tania Vanessa Arellano-Fernández
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  5. José Abel Lovaco-Flores
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  6. Aarón Espinosa-Jaime
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  7. J. Abraham Avelar-Rivas
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  8. Nelly Sélem-Mójica
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Corresponding author

Correspondence to Nelly Sélem-Mójica .

Editor information

Editors and Affiliations

  1. Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Jalisco, Mexico

    Alejandro Pereira-Santana

  2. Unidad de Biotecnología, Centro de Investigación CientÚfica de Yucatán, Mérida, Yucatán, Mexico

    Samuel David Gamboa-Tuz

  3. Unidad de Biotecnología., Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico

    Luis Carlos Rodríguez-Zapata

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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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Garfias-Gallegos, D. et al. (2022). Metagenomics Bioinformatic Pipeline. In: Pereira-Santana, A., Gamboa-Tuz, S.D., Rodríguez-Zapata, L.C. (eds) Plant Comparative Genomics. Methods in Molecular Biology, vol 2512. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2429-6_10

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  • DOI: https://doi.org/10.1007/978-1-0716-2429-6_10

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2428-9

  • Online ISBN: 978-1-0716-2429-6

  • eBook Packages: Springer Protocols

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