I am tasked with using biobakery tools to analyze a huge set of metagenomes from a public database, some of which are single end reads and some are paired end reads. I have no idea as to why this was done so I cannot speak to that choice (but I really wish it was all paired end!).
I was wondering if it’s possible to analyze single end and paired end reads together with Humann? Or, should I instead run paired end reads and single end reads separately through Humann (i.e., one Humann run for paired end reads, one Humann run for single end reads)?
There are likely differences in read length and sequencing depth between the paired end and single end reads, as well as sequencing quality, plus paired end reads tend to align more accurately compared to single end reads. However, I lose a ton of samples in my analysis if I only look at paired end reads.
All guidance, related to Humann and beyond, is welcome. Thank you so much everybody!