Kraken2 depletion for human reads as alternative to bmtagger

broadinstitute / viral-ngs

Viral genomics analysis pipelines

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Open yesimon opened 5 years ago

yesimon commented 5 years ago

Add kraken_unclassified command that combines p filtering with depletion
Less sensitive than bmtagger (tradeoffs) but much faster. Can be controlled with p. p=0.01-0.05 a close to bmtagger but not as aggressive.
Custom kraken2 needed to avoid executable name clashes with other kraken* packages.

tomkinsc commented 5 years ago

Does it make any sense to use this as a first pass to pare down data prior to running bmtagger?

yesimon commented 5 years ago

Not really because bmtagger is already fast enough. It's not going to deplete as many reads as bmtagger.