Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

test snpArcher #255

Open
amcooksey opened this issue Oct 31, 2023 · 1 comment
Open

test snpArcher #255

amcooksey opened this issue Oct 31, 2023 · 1 comment
Assignees
@amcooksey

Comments

@amcooksey
Copy link

https://snparcher.readthedocs.io/en/latest/index.html
https://github.com/harvardinformatics/snpArcher/blob/main/workflow/scripts/make_intervals.py
@amcooksey amcooksey self-assigned this Oct 31, 2023
@amcooksey
Copy link
Author

Documentation was updated to specify versions of both Python and Snakmake. Newer versions cause errors with F-strings that lead to spaces where there shouldn't be any.

I ran it on pecgos SRR18576017 (same as Szu-Ping's tool) with intervals set to 10 (chosen randomly, not optimized).
snpArcher: 36 hours
Szu-Ping's workflow: 50 hours

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@amcooksey amcooksey

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@amcooksey