Hello there! Can someone help me with a workflow for de novo assembly of a RNA virus (PRRSv).
Thank you a lot!
Please see the Galaxy Training Network for example workflows. https://training.galaxyproject.org/
Dockstore and Workflow Hub also have some examples, and more will be produced in the future.
Community contributions are welcomed at either site.
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Hi Jennaj,
thank you for this feed back. I was checking but I was wondering if there is some difference between bacterial assembly and Viral assembly. Thanks again !
@PhD_Nikolay_Anachkov viral assembly tends to be a whole lot simpler and can be done with, e.g., rnaviralSPAdes. Often, however, the question is whether it’s the best approach in general. Mapping to a reference might yield better consensus genomes with less manual curation effort if variability (especially recombination frequency) of viral isolates is only moderate. You could also find a middle ground like in Avian influenza viral strain analysis from gene segment sequencing data for AIV.
Don’t know enough about PRRSv to recommend one particular approach, but if you’d like to discuss more there’s the GalaxyProject Public Health room on Matrix: You're invited to talk on Matrix, which would be a good forum for this.
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This is extremely helpful. Thank you very much !