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NorwegianVeterinaryInstitute / irida-plugin-readsQC

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Decide on the tool for Contamination Check #5

Closed ajkarloss closed 2 years ago

karinlag commented 2 years ago

Hi! What do you want me to do here?

ajkarloss commented 2 years ago

Kraken2 or Mashscreen ?

I had a discussion with Håkon and Thomas.

Karkan2 is preferred over mashscreen.

  1. Kraken2+Bracken produces clean report and easy to interpret
  2. Mash Screen does not prodices a clean results with Species name
  3. We have a plugin which uses Kraken2 and Bracken so easier to develop
  4. Mash screen is faster compared to Kraken2 full database. We will use minikraken. Then the speed is comparable. The existing Kraken2 pipeline (Species abundance pipeline) in VIGAS takes about 4-5 minutes per sample.