K-Mer Analysis

Question

[vijay]

Can someone please explain me what a k-mer coverage of a sequence is? I have gone through a few forums explaining this concept but have not got a exhaustive idea still.

Appreciating ur valuable responses!!!

-Vijay

EDIT

Thanks for the response ..however I am not getting a cleat picture of Hash length,word length. Also I would like to know how K-mer impacts a sequnce assembly!!

Answer 1

[Leonor Palmeira]

A k-mer is a just a word of length k in a sequence. It is used in a variety of contexts, but you might some information in the following posts (probably in the second one):

• k-mers in de novo assembly algorithms (here)
• k-mer coverage (here)

Answer 2

[lgbi]

Maybe the these pages can help you a bit further:

• Maximizing Utility of Available RAMs in K-mer World
• An Explanation of Velvet Parameter exp_cov