Seed definition

[mido1951]

hello,

I wanted to know the definition of "Seed" and the construction of the "seed" in the genome assembly.
Do you have answers?

thank you for your help

[dpryan]

From context, it's a k-mer with which to begin graph traversal. The assemblies are (typically these days) made by splitting reads into subsequences of some length (k), processing those to clean them up, and then making a de bruijn graph out of them. For the last step, the vertices (k-mers) are stored but the edges typically not. One then choses a k-mer to start at and sees where it connects. Once you get to either a k-mer where you can't extend further or one where there's a branch*, you've hit the edge of a contig.

*One could conceive of many stopping rules, these are not exhaustive.