analysis of novel SARS-CoV-2 genomes

Question

[basuanubhav]

Hey all, so this question is not very specific because I have absolutely no idea about how to go about something like this.

We recently were able to assemble a few almost full length ( > 29kb ) contigs of SARS-CoV-2 from sequence reads originating from human tissue samples. NCBI BLAST using these sequences to the nt/nr database showed which entry in the database each contig was most closely related to and how many misatches were seen between them.

I was wondering that with a new SARS-CoV-2 sequence like ours, what all downstream analysis we can do and the tools/software/web apps required for the same. It would be nice to see where our sequences fit on the coronavirus lineage, their closest related strain and how the base changes ( non synonymous ) can potentially impact protein function etc. There is a HUGE amount of information on the web and it is really hard to understand how to start and go about this.

Any help will be truly appreciated.

Thanks in advance,

[GenoMax]

If you want to do this locally (if you don't want to upload the sequence) then Nextstrain has a tutorial available.

[basuanubhav]

Yes! I was going through the analysis and I'll give it a shot. In the meanwhile do you know any web apps where I can quickly upload my FASTA sequence and get some basic stats/figures etc?

Thanks a lot!!

[GenoMax]

You can try pangolin (LINK). There is a web application.

A search also brought up coronapp (LINK).

Answer 1

[Joe]

Your best bet would be to submit those sequences to one of the existing portals/databases such as GISAID, Nextstrain, or the CoG consortium.

They can take those sequences and compare them to all the existing data to place them on a tree, likely with a minimal amount of analysis required by you.