PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets.
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 (http://www.putonti-lab.com/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.
['Hatzopoulos|Thomas|T|', 'Watkins|Siobhan C|SC|', 'Putonti|Catherine|C|']
D001419:Bacteria D001435:Bacteriophages D016679:Genome, Viral D023281:Genomics D056186:Metagenomics D039002:Prophages D017422:Sequence Analysis, DNA D012984:Software
bacteriophage metagenomics prophage metaviromics virus whole genome sequencing