Patrick Cudahy
Hello, thanks for the great tool, it's been working well for me for a long time. However a week ago I traveled 6 time zones for work, but the scheduled...
Great book Hadley, I'm really enjoying it, but I think there's an issue with exercise 2 from 2.3.6 and from this [stack exchange question](https://stackoverflow.com/questions/55713549/) I don't think I'm alone. In...
I've got a set of 972 Mtb isolates that I'm trying to run `snp-sites -c -o` on, but it fails with the error `Warning: No SNPs were detected so there...
# Please fill out the issue checklist below, and provide all of the requested information. # Please always follow these steps: - [X] Confirmed this is a problem with `brew...
Hello Bo, thanks again for providing this excellent tool. I have a workflow where I build a custom database for `kraken` and then have a subsequent step that uses `kraken`...
Since upgrading to 0.22.3 (and similarly with 0.22.4) I've had issues using my HPC cluster. I've kept my notebook and hosts.yml file the same, so maybe I need to change...
I upgraded my jupyter installation and found that when using sos, the drop down menus in each cell to select the language were missing. I figured out that I had...
Silly question, but is it preferable to use `core.aln` or `core.full.aln` from `snippy-core` as the input to `snp-dists`, or even some other file output from `snippy`?
I've got a phylogeny that I'd like to annotate but am having issues. The annotation data is in the form of This code works: ``` p