Timothy Rozday

Bioinformatician at Sanger Institute, studying the infant gut microbiome.

[Robyn Wright @RobynJWright]

Q: Which is better for taxonomic classification of #metagenomics samples - Kraken2 or MetaPhlAn 3?

A: It really depends!

Read the very short story in this thread, or the full story in my preprint w/ @BetaScience and André Comeau: https://t.co/2U3e7odn8Y

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[Timothy Rozday @TRozdaySanger]

@RobynJWright @BetaScience Love this analysis. After doing my own tweaking I tend to go with 0.9 confidence threshold. Have you looked at min_hit_groups? I go with 40 for this, also useful for reducing misclassification