PhagePhisher
As the viral renaissance continues and researchers focus in greater depth on environmental viruses, it becomes clearer how complex a task it is to obtain meaningful viral information from large sequencing datasets. Currently, problems surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of information in existing genomic databases. PhagePhisher has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the collection and study of bacteriophages, viruses, and virally-related sequences, in a range of environments.
PhagePhisher's not just for phages! The pipeline can be applied to any NGS dataset to remove reads from contaminating DNA and assemble your genome of interest.
PhagePhisher's not just for phages! The pipeline can be applied to any NGS dataset to remove reads from contaminating DNA and assemble your genome of interest.
System Requirements: Everything you'll need is BioLinux or Unix-based OS with additional software. See Program Documentation for more details. (Note: version 1.2 released 12.16.2015)
Code and Readme:
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Code, Readme & Sample Data:
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You can access some of our data to test out PhagePhisher yourself:
- Search whole genome sequence data for phages! We've made some of our WGS data available online (beware it's a 1GB+ zipped file). With a background of bacterial genomes, you'll find phages (putative lysogenic and lytic phages alike) that were captured with bacterial cells (0.22um filter) from Lake Michigan nearshore waters.