Possible run with k gretter than 63

[kebern]

Hello,
I would want to run ska2 with k gretter than 63, for example k-mer=81 with in the middle SNP.

Is it possible to ugrade the ska2 with upgraded k?
I try k-mer=81 with ska1 but failed.
If no could you please advise other tools where k-mer value it up to 81.

Thank you.

KB.

[johnlees]

Max k=63 as that's the largest we can fit in u128, which is the longest base type in rust. It is possible to add longer precision but this would be a fair amount of work for us.

Can I ask exactly why you want to use a longer k-mer length? Typically you will get more recall with lower k, and we'd recommend 17 or 31.

[johnlees]

I actually think that SKA1 may work with any k-mer length so you could try that. Would still be interested to know why you want/need this

[kebern]

Thank you Johnlees.
I would like to have a possibility to work with gretter k (like k-mer=81), because at the end I can find the specific SNP for each node after build the tree. That will help to design primers and amplify the k-mer where is selected SNP.

[johnlees]

Ok interesting, thanks for sharing this.

Unfortunately we don't have the capacity to add this at the moment, but I'll leave this issue open – if lots of people want this feature we could consider adding it in future.

For now, I'd suggesting using SKA1: https://github.com/simonrharris/SKA

[kebern]

Thank you Johnlees.

BK.