Benjamin Callahan

@GiulianoColosimo Thanks for the ping on this. I am now in possession of an M1 Macbook Pro, so this is something I should revisit. All the x86 specific vectorized code...

@wolfganghuber Sorry for slow response. No this isn't solved yet. I do now have a working branch on my new M1 Mac, largely based on the previous PR by @terjekv:...

Sorry for this being delayed. This fix will be in (to natively compile on arm64 architectures like the M1) in the next release of dada2 this Fall. (And hopefully much...

We haven't implemented that logic, but this is a reasonable enhancement request to add a `repeats="deepest"` mode that performs as you describe. For now, you can do this in R,...

Hi Nico, On the topic of contaminants, you may want to take a look at our paper and [decontam software package](https://github.com/benjjneb/decontam) for dealing with contamination: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0605-2 That lays out our...

Then you can't just remove all the taxa you observe in the cross-contaminated negative control.

The recommended solution here would be to make a little custom R code prior to running the workflow, so it sounds like you are doing the right thing. If you'd...

> I was wondering if I should separate them before running dada2. It isn't necessary. You can run the data with both 16S + 18S sequences in it through DADA2...

All of the column names in your `ASVs` matris (the sequence table?) have the same empty string `""` name. This isn't a valid sequence table. It also appears to be...

That output suggests you are getting through the tutorial and generating a sequence table successfully. However, the large number of reads (>30\%) lost at the chimera stage typically indicate a...