Hi everyone, I would like to know how you usually deal with chimeras in 16S data, given that Kraken2 does not explicitly remove them (and, as far as I understand, it might actually handle them relatively well).
Here’s the dilemma I’m having with my colleagues: should we remove chimeras or not? Personally, I think it might not be strictly necessary because Kraken2 can classify them, but my colleagues argue that chimera removal is still required.
The problem is that if I remove chimeras, I need to work with ASVs (via DADA2), but then I can’t directly use Bracken afterwards for abundance re-estimation. This makes the pipeline inconsistent for relative abundance estimates.
My current workflow is basically: cutadapt > bbduk > bowtie2 > qiime2 > dada2 > kraken2 > krona > (bracken > krona ?)
Do you think chimera removal is still necessary in this case? How do you usually handle this when combining ASV pipelines with Kraken2/Bracken?
Curious as to why you have
cutadaptandbbduk.bbdukshould be able to do everything thatcutadaptcan (or vice versa). In the same waybowtie2(not sure why you have it there) could be easily replaced bybbmap. Flipping back and forth between programs sounds like more trouble.You are right. I initially decided to keep Cutadapt because I feel more confident using it for primer removal, and it is the tool most commonly found in QIIME2-based pipelines. Regarding the rest, I will follow your advice: I’ll remove Cutadapt and use the BBMap suite to handle adapter/quality trimming and host decontamination instead. Thanks a lot for the feedback!