Question: A couple questions about terminology in DSK --help
1
gravatar for rsharris
2.1 years ago by
rsharris20
United States
rsharris20 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 • 737 views
ADD COMMENTlink modified 2.1 years ago by Rayan Chikhi1.2k • written 2.1 years ago by rsharris20
0
gravatar for Rayan Chikhi
2.1 years ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k 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 COMMENTlink modified 2.1 years ago • written 2.1 years ago by Rayan Chikhi1.2k

Cool, thanks!

Bob H

ADD REPLYlink written 2.1 years ago by rsharris20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 755 users visited in the last hour