choice of k value for mapping my reads again a reference genome

Question

[StudentBio]

hello the community
I come back with my stupid question please excuse my ignorance:)
I want to map my reads single end on a reference genome with the smalt tool that ask me to enter the k value, and i don t khnow how can i chose this value, specifically this value must be between 3 and 20

[GenoMax]

What is the length of your reads? You could start with a value that is somewhere in the middle of 3 and 20.

Answer 1

[h.mon]

Optimal settings depend on genome and read sizes, the SMALT manual provides a lot of suggestions, in particular there is a nice table and a section titled Tuning performance on the last page.

[StudentBio]

when I used kmergenie, the optimal value of k was 81 but the smalt tool does not allow more than 20

[h.mon]

kmergenie suggests the optimal kmer to be used for assembly, not mapping.

[StudentBio]

i have read sizes between 25-403 and total sequence about 89 000 000 and size of the genome is about 295 000 000 please which kmer value I must adopt

[h.mon]

-k 13 -s 3 or -k 13 -s 4.