Young

These isolates were all amplified with the V4 primers (not 4.1) with 75 bp fragments ``` # UT-UPHL-220202309634 # UT-UPHL-220204125669 VIRUS DETECTION METRICS,UT-UPHL-220204125669,SARS-CoV2,+ VIRUS DETECTION METRICS,UT-UPHL-220204125669,SARS-CoV2 Kmers,57956 VIRUS DETECTION METRICS,UT-UPHL-220204125669,SARS-CoV2...

Notes : There are some aspects of the nf-core template that I'd like to avoid, such as defining variables in the config file in such a way that they can...

Guide for how to do this : https://github.com/apetkau/nf-core-assemblyexample

Appears to work fine 

Added wiki in https://github.com/UPHL-BioNGS/Cecret/pull/274

Roary is no longer maintained. (https://github.com/sanger-pathogens/Roary). I ran into many issues with Roary that several other people had also run into, such as having samples randomly being dropped from the...

I have good news! 1. I was able to replicate your findings Yay? 2. I also ran these files through ppanggolin, just to see if those results to be more...

Now for some bad news. I ran your samples by adjusting several of panaroo's parameters listed at https://gtonkinhill.github.io/panaroo/#/gettingstarted/params I didn't see a big difference in the core genome size. When...

Looks like I can't use bugseq, so I can't compare refmlst. It looks like it uses minimap2 to identify genes of interest and it maps reads onto those genes.

> Thanks for running all those tests, but still not a clear picture of what is going on here. I am surprised by the ppanggolin result showing everything within 0-1...