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

Assess CAG 'completeness' with CheckM #65

Open
sminot opened this issue Mar 4, 2021 · 0 comments
Open

Assess CAG 'completeness' with CheckM #65

sminot opened this issue Mar 4, 2021 · 0 comments
Labels
enhancement New feature or request

Comments

@sminot
Copy link
Collaborator

sminot commented Mar 4, 2021

Capturing an idea from @jgolob

Each CAG could be analyzed with CheckM to assess the degree of 'completeness' and 'contamination' for the CAG.

Quotes on those terms are applied since a CAG is not always expected to represent a complete or single genome, and so low levels of completeness or high levels of contamination are not always unexpected.

I haven't looked to see whether CheckM supports amino acid sequence input. If not, this may be a bit challenging to implement.
@sminot sminot added the enhancement New feature or request label Mar 4, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@sminot