what is k-mer coverage?

[Xueling Shu]

Hi all:

I guess this should not be a question for most of you. However I do not have a clue about the definition of "k-mer coverage". For instance if k-mer is defined as 32, then "k-mer coverage" means the ratio of number of merged reads to number of all the original reads?

Thanks!

Xueling  

[Shaun Jackman]

Hi Xueling,

If you were to split each read into its overlapping k-mer (with a step
size of 1), which would give you l-k+1 k-mer (where l is the length of
the read), and then mapped those k-mer to the contigs, the k-mer
coverage of a contig is the number of k-mer that map (with perfect
identity) to that contig.

Cheers,
Shaun

[Xueling Shu]

Thanks, Shaun!

Xueling