Counting k-mers shared between genome assemblies

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

genomics kmers

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updated 4.7 years ago by GenoMax

• written 4.7 years ago by gonzalez.pech.ra •

1 answer

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.

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written 4.7 years ago by GenoMax

Thanks for that!

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written 4.7 years ago by gonzalez.pech.ra •

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