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

Use Minimap2 for scaffolding instead of SortMeRNA #116

Open
ppericard opened this issue May 11, 2023 · 0 comments
Open

Use Minimap2 for scaffolding instead of SortMeRNA #116

ppericard opened this issue May 11, 2023 · 0 comments
Assignees
@ppericard
Labels
enhancement
Milestone
v1.7.0

Comments

@ppericard
Copy link
Member

SortMeRNA is designed to align short reads, Illumina type, and is used as the starting step in MATAM.
SortMeRNA is also used to re-align the assembled contigs onto the reference database to perform scaffolding. This is not optimal, and for scaffolding, SortMeRNA should probably be replaced by a more appropriate mapper such as Minimap2.
@ppericard ppericard added this to the v1.7.0 milestone May 11, 2023
@ppericard ppericard self-assigned this May 11, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@ppericard ppericard

Labels
enhancement
Projects
None yet
Milestone
v1.7.0
Development

No branches or pull requests
1 participant
@ppericard