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Identify parent lineages with RIPPLES #41

Closed
2 tasks
ktmeaton opened this issue Jun 24, 2022 · 2 comments
Closed
2 tasks

Identify parent lineages with RIPPLES #41

ktmeaton opened this issue Jun 24, 2022 · 2 comments
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@ktmeaton
Labels
enhancement New feature or request
Milestone
v0.4.0

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@ktmeaton
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I'd like to give RIPPLES another try, now that I'm more proficient with the matUtils commands.

Steps:

  • 1. Create a text file of cluster ids. This will be the first observed sequence for each recombinant lineage.
  • 2. Run ripples on those cluster ids.
@ktmeaton ktmeaton self-assigned this Jun 24, 2022
@ktmeaton ktmeaton added the enhancement New feature or request label Jun 24, 2022
@ktmeaton
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Running on the controls (N=60) with 32 cores, on the Public+GISAID tree (~10M) took 9.5 hours. Some options

  • Test v0.5.6. which is already on conda!.
  • Test ripples-fast (initially exited with segmentation fault).
  • Customize parameters to be less sensitive.

@ktmeaton
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Closing this in favor of Issue #46 since I'm having success with that approach currently.

@ktmeaton ktmeaton added this to the v0.3.1 milestone Jun 29, 2022
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@ktmeaton ktmeaton

Labels
enhancement New feature or request
Projects
ncov-recombinant
Status: Done
Milestone
v0.4.0
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@ktmeaton