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

Add amrfinder to atavide #5

Open
linsalrob opened this issue Jun 21, 2022 · 0 comments
Open

Add amrfinder to atavide #5

linsalrob opened this issue Jun 21, 2022 · 0 comments
Assignees
@linsalrob
Labels
enhancement New feature or request good first issue Good for newcomers

Comments

@linsalrob
Copy link
Owner

Add AMRfinder plus to atavide

The tool is found at AMRFinderPlus

You can find the tool at ncbi-amrfinderplus
See their [wiki](https://github.com/ncbi/amr/wiki/Install-with-bioconda]

Note: we need to consider adding protein calls (e.g. prokka?) and then using the AMRfinder plus HMMs. Note that genbank_to might help with the AMR finder GFF input
@linsalrob linsalrob added enhancement New feature or request good first issue Good for newcomers labels Jun 21, 2022
@linsalrob linsalrob self-assigned this Jun 21, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@linsalrob linsalrob

Labels
enhancement New feature or request good first issue Good for newcomers
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@linsalrob