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polyactis / Accucopy

Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
https://www.yfish.org/software/Accucopy
GNU General Public License v3.0
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Run on long reads data? #11

Open songbowang125 opened 3 years ago

songbowang125 commented 3 years ago

Hi, I want to use Accucopy on long read data, such as Pacbio or Nanopore. So I want to ask, whether your model fits long reads data or not. If yes, how can i set parameters like read_length and widow_size?

thanks.

fanxinping commented 2 years ago

Sorry to reply so late. You can try it on long read data. Accuopy will work in theory with default parameters.

husamia commented 11 months ago

@songbowang125 it's coverage based. large deletions will be the easiest. duplications if they are coverage will probably be easy too. those in between depends on your data, and weather your alignment is good. you want to combine with read based breakpoint detection