Window and K-mer size
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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
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.