Assembling multipartite (e.g. tripartite - 3 segments) viruses

Question

[bioinfo]

Hi all, I have sequenced (whole genome sequencing) a few isolates of a tripartite virus on MiSeq. I have done some preliminary assembly using SPAdes. I'm planning to obtain the "complete" genome for these isolates and make a comparative analysis. Since it is a tripartite genome how can I handle that?

[GenoMax]

Is tripartite referring to:

three regions that are 'functional and invariable', 'functional and variable' and 'non-functional and variable'

or something else?

tadpole.sh the k-mer based assembler from BBMap suite works well with viral genomes. You may want to try it.

[bioinfo]

Yes, "tripartite" refers to 3 different segments that the virus made of. I will look into Brian's BBMap suite. Thanks.

[Joe]

A "complete" genome doesn't need to be one continuous segment, it just means that any sections of DNA that are, in reality, contiguous, are represented as such in the final assembly.

I.e., a complete genome for a virus with 3 'chromosomes' should have 3 separate sequences. If you cannot obtain 3 from the MiSeq data (i.e. you're getting more contigs), then you will need to employ a long read technology to help scaffold against.