Benjamin Callahan

@emankhalaf I'm happy to provide support for the DADA2 package, and to some degree input/output from the package to others, but we don't provide support for analyses completely outside the...

It sounds like your issue here is with the behavior of cutadapt? If so, this might not be the best place to look for assistance. The one thing I can...

Is the number of detected primer sequences dramatically lower than there were present before cutadapt? Some residual primer hits might just be down to differences in pattern matching methods and...

There currently is not, but this could be an enhancement request. We have not really run into cases where this is the rate limiting step before, so haven't made it...

Thanks for the reports. I've added this issue to the 1.14 milestone, which is our next release in ~6 months. No promises, but it's at least on the formal agenda...

> Curious if there is now a beta version of the parallelized collapseNoMismatch command? This seems to be bottleneck in collapsing dozens of sequencing runs Nope there is not. But...

@ARBramucci Is this paired-end data? If so, the merged reads should cover the same genetic region (i.e spanning from primer to primer) even if the truncated forward/reverse read lengths were...

You shouldn't need to run `collapsNoMismatch` on normal data, including PacBio HiFi data that has had their primers consistently trimmed.

> if I hadn't trimmed primers, PacBio HiFi still would not need collapseNoMismatch? If you hadn't trimmed primes, you would have fundamental problems at the denoising step. The trimming to...

@ARBramucci No update other than this isn't a priority and probably won't be addressed in the near future. Note that if you have processed your data in such a way...