Alex Makunin

For me, it helped to fix a couple of additional versions during NGSpeciesID env setup: ``` conda install --yes -c conda-forge -c bioconda medaka==0.11.5 openblas==0.3.3 spoa racon minimap2 pysam==0.15.2 absl==0.9.0...

Hi @alexsweeten - as an option, would you consider generating Cooler files for interactive visualisation in HiGlass?

UPD - another place where qualities should be specified is DADA2_FILTNTRIM - `qualityType = "Auto"` is specified in `ext.args` section of module config as of ampliseq 2.11.0. I am also...

And another small update - unfortunately I won't be able to finish the test run. The reverse reads in my dataset had very low qualities, so did not pass DADA2_DENOISING...

Hi @d4straub - it seems that DADA2_QUALITY also auto-infers Phred score, but in a different way - `plotErrors` function [calls](https://github.com/benjjneb/dada2/blob/278f5f3ec03a846fe157b283cc08f2dd30430ae0/R/plot-methods.R#L159) `qa` function from `ShortRead` library - I could not figure...

Hi @d4straub, apologies for the delay. It seems that we might get proper paired end data soon. I'd prefer to provide that rather than just single end data - our...

Dear @d4straub - thanks for providing the update and pinging me, I'll aim to test this asap

Thanks so much @d4straub , the updated workflow works as expected and produces reasonable DADA2 outputs and QC plots with base qualities around 45-46. I've prepared test data of 1523...

Thanks @d4straub, PR created https://github.com/nf-core/test-datasets/pull/1477

Hi @d4straub, thanks again for looking into this. I'm utterly confused: both `d4straub/ampliseq -r add-param-for-phred-encoding` and `nf-core/ampliseq -r 2.11.0` correctly infer base qualities with the test data I've provided. I'm...