Kraken2 depletion for human reads as alternative to bmtagger #938
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Does it make any sense to use this as a first pass to pare down data prior to running bmtagger? |
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Not really because bmtagger is already fast enough. It's not going to deplete as many reads as bmtagger. |
Add support for krakenuniq, kaiju to replace kraken and diamond in default pipelines. Both rely on customized krakenuniq/kaiju packages for custom functionality, like loading database from pipe or printing out all taxa hits (kaiju). Krona fixed to use hit counts as scores in report files directly, instead of counting the individual read classifications (which takes a long time).
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* 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.
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kraken_unclassifiedcommand that combines p filtering with depletionclose to bmtagger but not as aggressive.