Question: Using SPAdes for assembling mitochondrial and viral genomes
0
gravatar for ropolocan
3.2 years ago by
ropolocan690
Canada
ropolocan690 wrote:

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.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by ropolocan690
2

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

ADD REPLYlink written 3.2 years ago by Sej Modha4.7k
1

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

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by GenoMax95k

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.

ADD REPLYlink written 3.2 years ago by ropolocan690
1

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

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by GenoMax95k

Thanks for your answer, @genomax!

ADD REPLYlink written 3.2 years ago by ropolocan690

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 :)

ADD REPLYlink written 18 months ago by macielrodriguez230
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