kraken2 is a taxonomy classifier, not an analysis platform, so cannot be compared to QIIME 2 itself (which is a software platform for building custom analysis workflows). The appropriate comparison is vs. q2-feature-classifier classify-sklearn naive Bayes classifiers with uniform taxonomic weights (the taxonomy classifier that was actually compared in that pre-print), not QIIME 2 or any of the other taxonomy classifiers or plugins available in QIIME 2.
Perhaps as a substitute for q2-feature-classifier (as another taxonomy classifier), but not for QIIME 2, as mentioned above.
From this point on it is worth acknowledging my biases, as a Q2 and q2-feature-classifier developer
Also full disclosure: I am not and was not in any way involved in the peer review of that pre-print, just in case anyone is speculating! But here’s my opinion:
That article shows some promising performance re: faster than q2-feature-classifier (not QIIME 2, the authors should have done better to differentiate these).
However, the authors’ own benchmarks show comparable accuracy to q2-feature-classifier, not better, so I disagree with that stated conclusion…
further, they compare vs. the standard classify-sklearn method using default uniform class weights to show comparable accuracy, we have already shown that using q2-clawback to build habitat-specific taxonomic weights can improve accuracy further… kraken2 would not capture those benefits:
Some final additional thoughts:
It would be great to see a kraken2 plugin! The faster runtime is an advantage, even if the accuracy is comparable to other methods. Ask the authors to make a plugin they can reach out to me directly for help.
- stand-alone kraken2 would break QIIME 2 provenance, losing one of the many advantages of QIIME 2: that processing decisions are recorded in provenance.
So if you are using QIIME 2 pipelines already, I’d recommend sticking with taxonomy classifiers in QIIME 2 to preserve provenance, unless if that faster runtime is critical (e.g., you are a service company and need to optimize turnaround time!). At least until a kraken2 plugin for QIIME 2 gets built, so that you can run kraken2 and preserve provenance