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Looks really great to me. Thanks so much @kbessonov1984
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Thank you for helping with this tool publication. It means a lot to Rebecca G. Hopefully the rapid typing provided by this tool will strengthen the epidemiological and surveillance of the Cryptosporidium parasite, allowing for better-informed public health decisions resulting in fewer people getting sick and improved targeted patient care. @bgruening We are excited to make this new version available. Hopefully it will appear in Galaxy Europe next week. This tool partially encapsulates knowledge and typing rules discussed in this publication https://www.sciencedirect.com/science/article/pii/S2667114X25000172 |
| <citation type="bibtex"> | ||
| @ARTICLE{RobinsonGp60, | ||
| author = {Robinson, Gillian and Chalmers, Rachel M. and Elwin, Kirsty and Guy, Richard A. and Bessonov, Konstantin and Troell, Kristina and Xiao, Lihua}, | ||
| title = {Deciphering a cryptic minefield: A guide to Cryptosporidium gp60 subtyping}, | ||
| journal = {Current Research in Parasitology and Vector-Borne Diseases}, | ||
| year = {2025}, | ||
| volume = {7}, | ||
| url = {https://doi.org/10.1016/j.crpvbd.2025.100257} | ||
| } | ||
| }</citation> |
There was a problem hiding this comment.
| <citation type="bibtex"> | |
| @ARTICLE{RobinsonGp60, | |
| author = {Robinson, Gillian and Chalmers, Rachel M. and Elwin, Kirsty and Guy, Richard A. and Bessonov, Konstantin and Troell, Kristina and Xiao, Lihua}, | |
| title = {Deciphering a cryptic minefield: A guide to Cryptosporidium gp60 subtyping}, | |
| journal = {Current Research in Parasitology and Vector-Borne Diseases}, | |
| year = {2025}, | |
| volume = {7}, | |
| url = {https://doi.org/10.1016/j.crpvbd.2025.100257} | |
| } | |
| }</citation> | |
| <citation type="doi">10.1016/j.crpvbd.2025.100257</citation> |
And above :)
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Enhanced CryptoGenotyper Galaxy Tool with FASTA support for Cryptosporidium typing
This Galaxy wrapper supports recent CryptoGenotyper v1.5.0 release with updated databases and improved error handling. The gp60 marker typing was updated as per publication https://www.sciencedirect.com/science/article/pii/S2667114X25000172
I also added extensive unit testing for contig mode which used a paired read collection.
More info on the release please see https://github.com/phac-nml/CryptoGenotyper/releases/tag/1.5.0