Counting k-mers shared between genome assemblies

Question

[gonzalez.pech.ra]

Hi there,

I am trying to count kmers shared between genome assemblies. I know this can be done with bbmap tools from this post. But I still have a few questions.

Can I get what I want from running the following?

kmercountexact.sh in=assembly1.fa,assembly2.fa,assembly3.fa out=shared_kmers.fa mincount=3

If I understand correctly, kmercountexact.sh already counts unique kmers per file. Or do I need to compress each assembly file with kcompress.sh before running kmercountexact.sh?

Thanks in advance!

Raúl

Answer 1

[GenoMax]

Yes you should run kcompress.sh individually as shown by @Brian. It will speed the process up, I would think. Depending of size of your assemblies you may need a lot of memory if you ran the countexact directly with fasta files. If you have small assemblies you could try that.

[gonzalez.pech.ra]

Thanks for that!