A couple questions about terminology in DSK --help

Question

[rsharris]

(I'm using DSK 2.0.6)

I don't understand the meaning of "solid" as it is used in the help listing. As in "solid kmers", "solidity", and "way to compute solids." I don't see the term used in the 2013 Bioinformatics manuscript. Can anyone clarify what this means?

A second question regards "minimizer". Is there more information about this somewhere?

Thanks for any help,

Bob H

Answer 1

[Rayan Chikhi]

Hi Bob, you're right, these terms were not defined in the readme!

A kmer is said to be solid if it occurs more than a minimal number of times in the dataset. DSK returns all the solid kmers (and their counts) as a result, and filters out all non-solid kmers. That threshold is set by the parameter "-abundance-min".

Minimizers are a technical objects we use during k-mer counting, following the KMC 2 algorithm. A typical user should not care about them. If you'd still like to know about minimizers, you can read more about them here : http://arxiv.org/abs/1407.1507

I've made some changes and the next release of DSK (2.0.8) will have an updated README and all command line parameters regarding minimizers will be in a separate "developer" section of the help so as not to confuse users.

Rayan

[rsharris]

Cool, thanks!

Bob H