Skip to content

Conversation

OndrejSladky
Copy link
Owner

@OndrejSladky OndrejSladky commented Mar 21, 2025

  • The global algorithm now first computes simplitigs (which is equivalent to merging on extensions of length 1) and the continues with the original implementation of greedy.
    • Preliminary results on s.pneumo genome:
      • ~4x speed up
      • ~3x memory savings
  • Additionally, KmerCamel now prints indicator progress.

The algorithm remains the same, but due to (possibly) different tie-breakings, the results may differ.

@PavelVesely
Copy link
Collaborator

PavelVesely commented Mar 21, 2025

To make it even better, and add the icing on the cake, it'd be great to see a progress messages / bar during the computation :-)

@OndrejSladky OndrejSladky merged commit 0c1bd7e into main Mar 24, 2025
3 checks passed
@OndrejSladky OndrejSladky deleted the ms_through_simplitigs branch March 24, 2025 14:37
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Add indication of computation progress Add info messages about individual phases
2 participants