Question: Using SPAdes for assembling mitochondrial and viral genomes
0
gravatar for ropolocan
16 months ago by
ropolocan500
Canada
ropolocan500 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 16 months ago • written 16 months ago by ropolocan500
1

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

ADD REPLYlink written 16 months ago by Sej Modha4.1k
1

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

ADD REPLYlink modified 16 months ago • written 16 months ago by genomax63k

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 16 months ago by ropolocan500
1

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

ADD REPLYlink modified 16 months ago • written 16 months ago by genomax63k

Thanks for your answer, @genomax!

ADD REPLYlink written 16 months ago by ropolocan500
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