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Freshwater Viromes: From Sampling to Evaluation

  • Catherine Putonti
  • Zoë Diener
  • Siobhan C. Watkins
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1849)

Abstract

There are a number of options available to researchers who wish to collect and analyze viral metagenomes (viromes) from environmental samples. Here we describe a laboratory procedure for generation of viromes from freshwater samples, specifically targeting dsDNA bacteriophages. We also discuss methods for bioinformatic analysis of the resulting data.

Key words

Viromes Metagenomics Freshwater viruses Bacteriophage Viral bioinformatics 

Notes

Acknowledgments

This work was supported by the NSF (1149387) (CP). The authors would like to thank all who assisted in previous studies mentioned here, including Katherine Bruder, Alexandria Cooper, Thomas Hatzopoulos, Alex Kula, Kema Malki, Zachary Romer, Jason Shapiro, and Emily Sible.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Catherine Putonti
    • 1
    • 2
    • 3
    • 4
  • Zoë Diener
    • 5
  • Siobhan C. Watkins
    • 5
  1. 1.Department of BiologyLoyola University ChicagoChicagoUSA
  2. 2.Department of Computer ScienceLoyola University ChicagoChicagoUSA
  3. 3.Bioinformatics ProgramLoyola University ChicagoChicagoUSA
  4. 4.Department of Microbiology and ImmunologyStritch School of Medicine, Loyola University ChicagoMaywoodUSA
  5. 5.Department of BiologyNew Mexico Institute for Mining and TechnologySocorroUSA

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