Extracting k-mer counts from multiple genome sequence files

Question

[yas]

Good day everyone, I am new here.

So, I have downloaded 8 completed genome fasta files for 8 strains of Bacillus subtilis spp.

My aim is to do classification based on their k-mer abundance profiles.

I am wondering, is there any tools that I can use to generate and extract the k-mer counts for each of the 8 genome files in a single output?

Answer 1

[Andrzej Zielezinski]

Two very popular tools specifically designed for k-mer counting:

1. KMC3 [tool] [paper]

2. Jellyfish [tool] [paper]

Other k-mer counting tools are listed in the benchmark study of k-mer counting methods.

[yas]

Thank you!

Answer 2

[5heikki]

Mash is an excellent tool for this kind of thing. It's far more sophisticated than simple k-mer abundance counting..

[yas]

Thank you so much for the answer. But I need to generate the k-mer abundance profiles.

Answer 3

[Matthias Zepper]

You could use kmercountmulti.sh from the BBTools Suite if you are specifically interested in k-mers.

[yas]

Thanks for the suggestion.