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Question: A couple questions about terminology in DSK --help
1
gravatar for rsharris
2.8 years ago by
rsharris • 20
United States
rsharris • 20 wrote:

(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
dsk • 889 views
ADD COMMENT • link •
modified 2.8 years ago by Rayan Chikhi • 1.3k • written 2.8 years ago by rsharris • 20
0
gravatar for Rayan Chikhi
2.8 years ago by
Rayan Chikhi • 1.3k
France, Lille, CNRS
Rayan Chikhi • 1.3k wrote:

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
ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by Rayan Chikhi • 1.3k

Cool, thanks!

Bob H

ADD REPLY • link written 2.8 years ago by rsharris • 20
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