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

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

smalt k-mers mapping
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updated by Ram Ram • written by StudentBio • StudentBio

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

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written by GenoMax GenoMax

1 answer

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.

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written by h.mon h.mon

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

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written by StudentBio • StudentBio

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

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written by h.mon h.mon

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

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written by StudentBio • StudentBio

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

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written by h.mon h.mon

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