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Quality filters for the core gene phylogeny #37

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3 tasks
zachary-foster opened this issue Nov 9, 2023 · 1 comment
Closed
3 tasks

Quality filters for the core gene phylogeny #37

zachary-foster opened this issue Nov 9, 2023 · 1 comment

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@zachary-foster
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Three user-adjustable filters:

  • --min_core_genes: Minimum number of core genes (e.g. 10)
  • --min_core_samps: Minimum proportion of samples (e.g. 0.9)
  • --min_core_refs: Minimum proportion of references (e.g. 0.5)

Plan:

Iteratively remove sample with the least genes shared with all other samples until --min_core_genes is reached or --min_core_samps/--min_core_refs thresholds are reached.
@zachary-foster
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done

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