====== glsearch validation ======


K-mers produced by //keeSeek//, which have a minimum required distance from the relative reference sequences, have been validated by using an external tool. 
We have chosen glsearch (version 36.3.5b) ([[http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=keeseek:references|Pearson, 2000]]), a global-local aligner part of the Fasta3 package and based on the Needleman and Wunsch algorithm [[:keeseek:references|(Needleman and Wunsch, 1970]]). The glsearch command line used is the following:


<file>
glsearch36 <query> <reference> -f -100 -g -100 -n -b 1 -d 1 -E 10000 -z -1
</file>


Note that, to make the results from //keeSeek// and glsearch comparable, we heavily penalize gap extension (-g parameter), to avoid their presence in the final output.