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DIAMOND +  MEGAN Microbiome Analysis

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Metagenomic Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2649))

Abstract

Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments. The resulting classifications can then be interactively analyzed and compared. Here we illustrate how to pursue this approach using the DIAMOND+MEGAN pipeline, on two different publicly available datasets, one containing short-read samples and other containing long-read samples.

Authors Anupam Gautam and Wenhuan Zeng equally contributed.

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Acknowledgements

The authors acknowledge hardware support by the High Performance and Cloud Computing Group at the Zentrum für Datenverarbeitung of the University of Tübingen, the state of Baden-Württemberg through bwHPC, and the German Research Foundation (DFG) through grant no. INST 37/935-1 FUGG. We would also like to acknowledge Marius Eisele for helping us with the long-read datasets.

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Authors and Affiliations

  1. Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany

    Anupam Gautam

  2. International Max Planck Research School “From Molecules to Organisms”, Max Planck Institute for Biology Tübingen, Tübingen, Germany

    Anupam Gautam

  3. Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany

    Wenhuan Zeng & Daniel H. Huson

Authors
  1. Anupam Gautam
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  2. Wenhuan Zeng
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  3. Daniel H. Huson
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Corresponding author

Correspondence to Daniel H. Huson .

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Editors and Affiliations

  1. Leeds Institute of Medical Research, University of Leeds, Leeds, UK

    Suparna Mitra

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Gautam, A., Zeng, W., Huson, D.H. (2023). DIAMOND +  MEGAN Microbiome Analysis. In: Mitra, S. (eds) Metagenomic Data Analysis. Methods in Molecular Biology, vol 2649. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3072-3_6

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  • DOI: https://doi.org/10.1007/978-1-0716-3072-3_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3071-6

  • Online ISBN: 978-1-0716-3072-3

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