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Add virus kraken reclassification #75

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rmcolq opened this issue Nov 14, 2024 · 1 comment
Closed

Add virus kraken reclassification #75

rmcolq opened this issue Nov 14, 2024 · 1 comment

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@rmcolq
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rmcolq commented Nov 14, 2024

with custom virus database
@rmcolq
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rmcolq commented Nov 29, 2024

This is added in PR #81 - allows a second (viral) kraken database to be used for those identified as viral/unclassified with the first database. Workflow is then

  1. Classify with big database
  2. Optionally, extract viral+unclassified fraction from this, run viral database on the subset, merge kraken reports+assignments
  3. Use the (merged) kraken assignments and reports to continue with the HCID/spike detection, read taxa/fraction extracting and report generation

@rmcolq rmcolq closed this as completed Nov 29, 2024
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