Help needed to bulid Pylogenetic analysis for viruses

1

Hi All,

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.

Thank you.

2

I recommend downloading the GISAID dataset: nextfasta and nextmeta. These files are in the necessary format for carrying out nextstrain.

3

Hi @nitha – I would recommend looking through the Snakefile of the zika tutorial in conjunction with the tutorial which should explain the commands being run.

In terms of CDS vs complete genome, the answer is “it depends”. It’s possible to create phylogenies for either, however the appropriate approach is dependent on the characteristics of the virus you are analysing.