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Analyses of Nuclear Reads Obtained Using Genome Skimming

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DNA Barcoding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2744))

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Abstract

In this protocol paper, we review a set of methods developed in recent years for analyzing nuclear reads obtained from genome skimming. As the cost of sequencing drops, genome skimming (low-coverage shotgun sequencing of a sample) becomes increasingly a cost-effective method of measuring biodiversity at high resolution. While most practitioners only use assembled over-represented organelle reads from a genome skim, the vast majority of the reads are nuclear. Using assembly-free and alignment-free methods described in this protocol, we can compare samples to each other and reference genomes to compute distances, characterize underlying genomes, and infer evolutionary relationships.

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Author information

Authors and Affiliations

  1. Electrical and Computer Engineering, University of California—San Diego, La Jolla, CA, USA

    Siavash Mirarab

  2. Computer Science and Engineering, University of California—San Diego, La Jolla, CA, USA

    Vineet Bafna

Authors
  1. Siavash Mirarab
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  2. Vineet Bafna
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Corresponding author

Correspondence to Siavash Mirarab .

Editor information

Editors and Affiliations

  1. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA

    Robert DeSalle

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Mirarab, S., Bafna, V. (2024). Analyses of Nuclear Reads Obtained Using Genome Skimming. In: DeSalle, R. (eds) DNA Barcoding. Methods in Molecular Biology, vol 2744. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3581-0_16

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  • DOI: https://doi.org/10.1007/978-1-0716-3581-0_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3580-3

  • Online ISBN: 978-1-0716-3581-0

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