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schatzlab / genomescope

Fast genome analysis from unassembled short reads
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how to ensure k-mer value #25

Closed GeorgeBGM closed 5 years ago

GeorgeBGM commented 5 years ago

Hi, I want to assembly a small region of human chromosome Y, what should I do to choose a reasonable k-mer? You known that we often use 21-mer to assembly human genomics, but how I just want to de novo a small region of human chromosome Y, do you think the 21-mer is ok?or I need to calculate new k-mer as formula：k = log4 (G(1−p)/p)（https://www.ncbi.nlm.nih.gov/pubmed/15087315?dopt=Abstract&holding=npg） Thanks for your patient. Best Duo

mschatz commented 5 years ago

If you have really isolated a small region you could probably use a smaller k value as you suggest. This is pretty straightforward for a simulation, but will be hard to do experimentally except if you were to isolate and amplify a bacterial artificial chromosome (BAC) or fosmid library.

Good luck

Mike

GeorgeBGM commented 5 years ago

Hi, Mike Thanks for your advises,I will attempt it. Best, Duo