Genome Assembler for Transcript Assembly

Question

[kilcdincer]

Hello,

Can genome assembler be used for transcript assembly?

Thanks very much!

Answer 1

[Mensur Dlakic]

There are genome assemblers with some kind of --rna or --est options that can be used for transcriptome assembly. MIRA and SPAdes would be in that category, and I am sure there are others.

If you are asking if ANY genome assembler can be used, I'd say probably yes, but it would not necessarily be a good idea.

[kilcdincer]

Thanks very much for your reply.

Are you familiar with MaSuRCA? Do you think it can be used for transcript assembly?

[Mensur Dlakic]

Never used it. It should say clearly on their web page what it can be used for.

[kilcdincer]

Yes, I checked but I wanted to confirm since I was said the opposite of what I have found on its paper and manual. I supposed I was missing something. Thanks very much!