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PhagePhisher: a Pipeline for the Discovery of Covert Viral Sequences in Complex Genomic Datasets
Microbial Genomics
  • Thomas Hatzopoulos, Loyola University Chicago
  • Siobhan C Watkins, Loyola University Chicago
  • Catherine Putonti, Loyola University Chicago
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Microbiology Society
Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher ( has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with limited operator knowledge of bioinformatics on a standard workstation. As a proof-of-concept, PhagePhisher was successfully implemented with bacteria–virus mixed samples of varying complexity. Furthermore, viral signals within microbial metagenomic datasets were easily and quickly identified by PhagePhisher, including those from prophages as well as lysogenic phages, an important and often neglected aspect of examining phage populations in the environment. PhagePhisher resolves viral-related sequences which may be obscured by or imbedded in bacterial genomes.

Author Posting © Microbiology Society, 2016. This article is posted here by permission of the Microbiology Society for personal use, not for redistribution. The article was published in Microbial Genomics, Vol. 2, Iss. 3, March 2016,

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Creative Commons Attribution-Noncommercial 4.0
Citation Information
Thomas Hatzopoulos, Siobhan C Watkins and Catherine Putonti. "PhagePhisher: a Pipeline for the Discovery of Covert Viral Sequences in Complex Genomic Datasets" Microbial Genomics Vol. 2 Iss. 3 (2016)
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