Code, scripts, some logs and general misc. from to the RNA viruses in MetaTranscriptome discovery project (a.k.a RVMT), openly shared near the time of submission.
Note! The scripts: get_polyproteins.ipynb and get_clan_membership.ipynb Mentioned in the paper, are availble over in a companion bitbucket repo(due to some bureaucracy, we couldn't have those scripts on GitHub, but hopefully whoever is interested in them could find them useful just the same over in the bitbucket repo).
This repos consolidates scripts, code and various snippets used throughout the RVMT project. Many of these are custom, and the code is provided mostly for the purposes of disclosure rather than as a product. The scripts are heavily environment-dependent and are not likely to be able to work on other platforms without extensive modification.
While we make no promise regarding the portability of this ensemble, should you want to try and make use of these, please do, they are FOSS after all, and feel free to let us know, we'll be happy to try and help out.
Data from the project is deposited in Zenodo DOI:10.5281/zenodo.7368133.
The project is described by the DOI:10.1016/j.cell.2022.08.023, which you can cite as:
Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjamin Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene V. Koonin, Uri Gophna. 2022. “Expansion of the Global RNA Virome Reveals Diverse Clades of Bacteriophages.” Cell, September, S0092867422011187.