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16S Databases giving different results

I am doing a comparative study between different metagenomics classifiers, and I downloaded different 16S databases (SILVA,RDP and greengenes) which were used for building both centrifuge and kraken2 with same files. I ran both classifiers with the default settings for both and same input files (Filtered fastq) obtained with 16S barcoding kit ONT and sequenced on MinION device. But each classifier gave different results when using same database. What is causing this difference?

database 16s kraken.centrifuge nanopore
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updated by andres.firrincieli andres.firrincieli • written by abraams • abraams

i used 2 different classifiers: kraken2 and centrifuge

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written by abraams • abraams

Sorry abraams I totally missed that part. This is not unexpected since centrifuge and kraken2 use two entirely different classification algorithms. However, starting from the same 16S database the type of species identified by kraken2 and centrifuge should be the same.

ps. greengenes is outdated. Do not use it

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written by andres.firrincieli andres.firrincieli

thank you andres for your reply, i used same files to build database for both calssifiers but they gave different results

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written by abraams • abraams

is it possible that the differences you see between centrifuge and kraken2 are more noticeable when you look at the results at lower taxonomic levels i.e. genus or species?

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written by andres.firrincieli andres.firrincieli

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