Minimap2 algorithm : seed-chain-align

Question

[KVC_bioinfo]

Hello all,

I am trying to understand the algorithm of Minimap2. Here, so far I understand follows a typical seed-chain-align procedure. However, I did not understand for seeding how the k-mers are selected and how long are they?

Could someone help me understand it?

[WouterDeCoster]

Question cross-posted at https://github.com/lh3/minimap2/issues/60

[KVC_bioinfo]

Yes, In the interest of understanding it I have reached there. If this is not allowed I will close the question.

Thank you.

[WouterDeCoster]

I think it should be allowed - but don't forget to add links in that case.

We don't want that someone else spends a lot of effort here only to find out later that the question already received an answer on GitHub.

[KVC_bioinfo]

Sure. Thank you. I will take care of next time.

Answer 1

[KVC_bioinfo]

I found the answer.

"With normal k-mer, the k-mer size is specified on the command line. It varies with presets."