Using SPAdes for assembling mitochondrial and viral genomes

Question

[ropolocan]

Hello,

I have been assembling mitochondrial genomes with SPAdes, and I have been getting good assemblies. However, someone brought to my attention that SPAdes is optimized for bacterial genomes. I have also assembled viral genomes with SPAdes.

Is SPAdes optimized for bacterial genomes? If it is, how so? Is it appropriate to use it for assembling mitochondrial and viral genomes?

Thanks.

[Sej Modha]

I have always used SPAdes for viral genomes and it has produced good assemblies.

[GenoMax]

You can try tadpole.sh from BBMap for small (viral) genomes. Guide here.

[ropolocan]

I will consider it, thanks. Do you think it would be appropriate to use tadpole.sh for mitochondrial genomes? The mitogenomes I am working with are ~17Kb.

[GenoMax]

Sure. It should be fast as well. Make sure your input are not contaminated with other data.

[ropolocan]

Thanks for your answer, @genomax!

[macielrodriguez2]

Hi! I'm assembling a mitogenome of 569,630 bp. I'm using SPAdes with 60x coverage and k-mers 47,57,67,77. I got 46 contigs. Then I used tadpole with 100x coverage and k=100 and got 222 contigs. I think that my main problem is that I'm not using the correct values for coverage and kmers.

Does anyone has some advice about this? Thanks a lot in advance :)