Katherine Eaton
Katherine Eaton
This PR adds the necessary files to: 1. Create a docker container 1. Create a Gitpod workspace I was trying to add a new feature to snippy, and got caught...
## Description I'm tackling the issue of sampling bias in mugration, and was curious if a p-value might be of use here? If I knew the probability of an event...
Is there a way to make analyses reproducible, perhaps by setting a random seed? Specifically, I'm using the ```run``` function of the ```TreeTime``` class to estimate a clock model. I've...
**Describe the bug** The calendar won't display if certain values are specified for `startTime`/`endTime` in the yaml frontmatter. **Steps to reproduce** Ex. Calendar displays correctly: ```yaml date: 2022-03-14 startTime: 09:00...
- I've seen one example so far where samples with the exact same node placement have different clade/lineage assignments. - The base tree in this example is public-latest (2022-04-17). -...
This week (2022-04-17), I noticed the [public trees](http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/) have a new(?) nomenclature for recombinant lineages that takes the format `miscBA1BA2PostX`. Some specific examples: - `miscBA1BA2Post8393` | EPI_ISL_11360224 - `miscBA1BA2Post17k` |...
**Description** Is the `ncbigenomedownload` module still available as in the [documentation](https://bactopia.github.io/v3.0.0/bactopia-tools/ncbigenomedownload/)? I keep getting the error `ncbigenomedownload is not a known workflow`. **Steps to Reproduce** ```bash # Install micromamba create...
Hello, Would it be possible to have the final confidence score reported in the output for each read? I'm exploring the use of this metric in calculating summary statistics for...
### Description of proposed changes I'm running into a problem when running multiple config files on different input data (ex. hmpxv1 vs. mpxv, or Nextstrain vs. LAPIS). Since the input...
- I've been experimenting with a flag `--ignore-shared` that ignores positions that are shared (have the exact same nucleotide) across all parents/examples. - I like this option because it makes...