Hi everyone,

I am using Kraken on a set of Illumina reads from a metagenomics project. In the past I have used dada2 for 16S amplicons and had to deal with chimera filtering. My question is the following, does a chimera removal step need to be performed before running Kraken or does Kraken manage the chimeras by itself? If I have to filter chimeric sequences, could anyone provide me a pipeline that gives me a Kraken compatible output?

I have tried reading about this but I am not able to find anything about it in the Kraken manual.

Thank you very much in advance.

Alan.