Chris Fields

@benjjneb I can add a link here, it's essentially a modified version of `mergePairs`: https://github.com/h3abionet/TADA/blob/dev/templates/MergePairs.R#L6 (note this is in a Nextflow template file for generating a R script, so there...

> I do expect to get a request in the future (as we have in the past) for the kind of functionality you have implemented. Is there anything more descriptive...

@effelsbn how are you processing the data (e.g. trimming, denoising, running chimera detection, etc)? If I'm reading this right, it looks like you had some loss at two stages, primer...

@effelsbn I'd have to go back and check but IIRC that stage is pretty stringent (triages reads if both primers aren't found); our Shoreline run does the same. I agree,...

**EDIT:** See also issue #1375 Just a note for the adventurous types trying to compile dada2 native M1, you can get part of the way there by installing the M1-compiled...

@LaurCC we do this quite frequently w/ [Fluidigm-generated data](https://biotech.illinois.edu/htdna/services-equipment/amplicons) where we get up to 24 amplicon pairs; I'm guessing this is similar? We basically demultiplex by sample _and_ primer pair...

@LaurCC if you want to run each PCR primer pair through DADA2 independently and if your PCR rxns are pooled and barcoded by sample (like our case), you'd need to...

There appears to be a fork that deals with this as well as a pull request, #619. @tseemann I'm not sure if that could be pulled in?

Checklist (some are already in place) **Modules** - [x] alignment (accelerated bwa) - [ ] BQSR (optional?) - [x] DNAseq (SNV/Indel) - including GVCF support - [x] DNAscope (SV and...

> Sentieon has that if I remember well Correct; it also supports VQSR though I'm not sure if that's on the roadmap here, I've been running it separately.