Young

I'm a little torn about what to do with this one. 1. I only use this image for POLCA 2. But I've been moving to pypolca 3. But what about...

Is there a recommended way to edit the xml file or download script?

> add option to down-sample reads, because sometimes this can actually improve assembly Filtlong can down-sample reads to the longest/highest quality reads and rasusa can downsample randomly. I know there...

Another idea I recommend adding is a rotation step. This ensures all bacterial chromosomes at least start at dnaA. A case-in-point. These are two chromosomes from a clonal outbreak. They...

For Assembly QC, I'm a fan of gfastats for metrics about the created gfa files and nanoplot. They have a lot of overlapping features, but gfastats does indicate if a...

Here's a blog post from Dr. Wick about depth and quality : https://rrwick.github.io/2023/11/06/accuracy-vs-depth-update.html > You can see in the plot that accuracy improved up to ~100× depth, after which additional...

Actually, what I need is a github release. That way I can wget or curl your repo.

I need something in here (when it's ready): https://github.com/lenaschimmel/sarscov2recombinants/releases

@lenaschimmel Let me look those sequences up

The consensus fastas for the following sequences were generated were generated from single-end Illumina reads with the dragen pipeline. ``` submission_id,sra_id UT-UPHL-220202309634,SRR17916009 UT-UPHL-220204125669,SRR17977717 UT-UPHL-220204444755,SRR17977317 UT-UPHL-220204978864,SRR17977192 ``` I'm off to find...