Humann3 Paired end reads


I’m just wondering how HUMAnN3 handles paired-end reads? I’m pretty new to metagenomics data analysis and was wondering if you can help.


I’ve written a bit about this here:

In short, we recommend concatenating your paired reads upstream of MetaPhlAn and HUMAnN.

Hi… Is it necessary to run kneaddata before running MetaPhlAn 3.0 even if I use
--ignore_eukarya option with metaphlan command?

--ignore_eukarya will only ignore reads recruited to eukaryotic microbial marker genes; it will not ignore/exclude generic human contaminant DNA. That said, MetaPhlAn itself is fairly robust to un-removed human contamination, but downstream steps (e.g. HUMAnN’s translated search) might not be.

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In other words,whether to merge two files directly?for example:

cat sample_R1.fq sample_R2.fq > merge_sample.fq


Correct, this is what we mean when we say to concatenate paired reads.