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analysis of novel SARS-CoV-2 genomes

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,

processing phylogenetics analysis covid19
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updated by GenoMax GenoMax • written by basuanubhav • basuanubhav

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

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written by GenoMax GenoMax

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!!

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written by basuanubhav • basuanubhav

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

A search also brought up coronapp (LINK).

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written by GenoMax GenoMax

1 answer

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.

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written by Joe Joe

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