Is kraken2 suitable for tNGS data?

[zhuying412]

I know that Kraken2 is commonly used for metagenomic data analysis and species classification. I wonder if it is suitable for tNGS (targeted Next-Generation Sequencing) data, such as data obtained from ultra-multiplex PCR capture or probe capture?

[jmonroynieto]

Yes you can use it with manual definitions. I do this regularly but have never tried to do it with small targets. Because kraken is designed as a taxonomic classifier, I also would recommend that you be very mindful of your objective and the underlying differentiators.

Are you targeting a barcoding sequence? Are you using a set of unique genes for a taxon? Are you wanting to do presence/absence detection for a multiplexed assay?