Window and K-mer size

[HTaekOppa]

Hi MashMap,

Hope this email finds you well.

Just wondering is it possible to indicate a specific window size? Or, is it automatically calculated based on segment length?

From the "mashmap -h", I can see the -k (kmer), -s (seg length) and --pi (percent identity) can be modified but not the "Window Size".

I am trying to calculate the percentage of each 2Mb region (I assume this part would be "Window Size") covered by a query sequence of at least 1,000bp (I assume this part would be "seg length) and 95% identity (I assume this part would be "percent identity").

Looking forward to your reply!

Cheers,

Taek

[cjain7]

Just wondering is it possible to indicate a specific window size? Or, is it automatically calculated based on segment length?

Yes it is automatically computed.

Your interpretation of seg length and percent identity is correct, but window-size is a parameter for kmer sampling, it shouldn't be changed for your application. The way minimizer-based k-mer sampling works is that we pick minimum k-mer within a window; this helps towards better speed and memory-usage of the algorithm. So you can specify your ref. and query, and seg length of 1000 bp, I think it should work out.