I would like to do phylogenetic analysis and build a phylogenetic tree for RNA viruses as well to identify the mutations in strains using NextStrain tool. From the tutorial, I understood basically we need 2 files to start Nextstrain. 1. sequence.fasta and 2. Metadata. I am confused about what type of sequence should be download from NCBI (whether it is a Complete genome or CDS)?
2. What is the augur filter, in what bases I have to exclude the sequence?
3. how these “config” folder files are created? whether they automatically created while running NextStrain Steps?
Sorry, I couldn’t understand properly how to use nextstrain efficiently when I am are trying to build a phylogenetic tree analysis for a virus strain. Could anyone please guide me on how to do it?
I am able to run zika and other tutorials but not to create my own.