Tree customization - set min_date

Help and Getting Started
1

Hi Nextstrain team,

I tried to set a min-date for my custom tree on auspice, but none of the following commands in the builds.yaml file worked out:

filter:
  min_date: 2021-08-01
#or
  min_date: "--min-date 2021-08-01"

#or
augur filter:
  min_date: 2021-08-01
#or
  min_date: "--min-date 2021-08-01"

Thanks in advance for looking into this!

2

Hi @ralfduerr – what was the error that you saw, or what was produced by the build indicating it didn’t work?

The syntax for defining a minimum date filter as part of the ncov workflow can take on two forms:

filter:
  min_date: 2021.123
# or
filter:
  min_date: 2022-01-01
3

Hi James,

The filter actually worked in the augur pipeline when filtering query sequences, so this part is resolved, but in addition to that, I was wondering whether there’s a chance of selectively displaying a tree with defined min and max dates in auspice?
(I could only find that option for the video)

Many thanks!
Ralf

4

Yup! You can choose a time slice in Auspice via the date sliders in the sidebar. This also updates the URL so you can share this and load the visualisation at that time slice. Here’s an example for zika: nextstrain.org/zika/?dmax=2015-05-17&dmin=2013-10-02

image
image1076×447 55.4 KB

5

I see but the other regions are just grayed out. Is there an option to expand this selection to the entire screen to get a better resolution on the x-axis/time scale?
I know there’s the possibility to click on a branch to enlarge the respective subtree, but if there are multiple branches, it would be great to be able to expand the entire slice. Is that possible?
Thanks!

6

Not yet possible, but improving tree zooming functionality is high on our to-do list…

7

Super!
Thank you, James.