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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads

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Reproducibility of results

dlavrov opened this issue · comments

commented

Question or Expected behavior
I ran NextDenovo three times using the same control and input files and it produced three different assemblies that varied in the number of scaffolds (159-181), the total size 157-160Mbp and the size of the largest scaffold 6-13 Mbp. What is the reason for this variation and is there any way to make the assembly reproducible (e.g., by entering a "random" number)?

Operating system
Red Hat Enterprise Linux Server release 7.9 (Maipo)

NextDenovo
What version of NextDenovo are you using?
2.5.0

commented

Hi, it is hard to make the assembly reproducible, two reasons,

  1. Some multi-thread modules have different output order each time.
  2. Unstable sorting algorithms are widely used by NextDenovo.