Question: Does rnaSPAdes represent a convenient assembler for RNA viruses?
gravatar for Guillermo D. Huerta
2.2 years ago by
Columbus (Ohio)
Guillermo D. Huerta10 wrote:

Hi all,

I am wondering if rnaSPAdes represents a convenient assembler for RNA viruses (from metagenomes or metatranscriptomes). As far as I know, rnaSPAdes cannot be set in any other kmer than 55mer. On the other hand, metaSPAdes can be set in several (also smaller) kmers. Is this feature making the latter a more convenient assembler for extracting RNA viruses from datasets?

Let me know what you think please. Thanks!

kmer rna virus spades assembly • 585 views
ADD COMMENTlink written 2.2 years ago by Guillermo D. Huerta10

I never used rnaSPAdes nor metaSPAdes for viral assembly, but used Trinity, which also uses a fixed kmer. It worked fine every time I used, but in general, it is necessary a second round of assembly with CAP3 to get the complete viral genome.

ADD REPLYlink written 2.2 years ago by h.mon31k
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