Thanks for providing such an important training session ( From NCBI’s Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis). I learned a lot from the Galaxy platform.
When I processed the step ’ Annotate variant effects with **SnpEff eff’, the system reminded me to load genome information. Could anyone help me to show where to find this file for the Covid-19 virus?
The tutorial is a bit ambiguous at that step (and should get updated to clarify things).
It assumes you’re using the covid-19 edition of SnpEff, which has the same tool name, SnpEff eff, but the description “annotate variants for SARS-CoV-2”. This comes as a separate tool in the tool panel.
This special version comes with various SARS-like genome annotation files preinstalled and the default, NC_045512.2, is the one you want.
Thanks for the report!