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Preprint

Database construction

DR Daniel A Russell
GH Graham F Hatfull

Last updated date: May 12, 2021 Views: 898 Forks: 0

original An abbreviated version of this protocol was published in eLife in Apr, 2015
Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity
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We use a suite of tools locally to perform database construction called pdm_utils. They're publicly available on github. 

https://github.com/SEA-PHAGES/pdm_utils

The usage and structure are detailed in the docs.

https://pdm-utils.readthedocs.io/en/latest/

There's also a tool for database construction called PhamDB, which may be easier to use for the end-user who doesn't want to create a whole pipeline as in pdm_utils.

https://github.com/jglamine/phamdb

 

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Russell, D and Hatfull, G(2021). Database construction. Bio-protocol Preprint. bio-protocol.org/prep1080.
  2. Pope, W. H., Bowman, C. A., Russell, D. A., Jacobs-Sera, D., Asai, D. J., Cresawn, S. G., Jacobs, W. R., Hendrix, R. W., Lawrence, J. G. and Hatfull, G. F.(2015). Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife. DOI: 10.7554/eLife.06416

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