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.

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

Add UniverSC aligner to support other technologies #170

Closed
TomKellyGenetics opened this issue Oct 24, 2022 · 2 comments
Closed

Add UniverSC aligner to support other technologies #170

TomKellyGenetics opened this issue Oct 24, 2022 · 2 comments
Assignees
Labels
enhancement New feature or request

Comments

@TomKellyGenetics
Copy link
Member

Description of feature

Expands functionality of Cell Ranger as explained here #31

Implements an open-source alternative (not subject to 10X EULA) which supports other single-cell transcriptomics platforms.

See detailed discussion here:
nf-core/demultiplex#14
nf-core/modules#1644
nf-core/modules#1706

Module details:
GitHub repo: https://github.com/minoda-lab/universc
Docker container: https://hub.docker.com/r/tomkellygenetics/universc
Preprint: https://www.biorxiv.org/content/10.1101/2021.01.19.427209v1 (accepted for publication in Nat. Commun. in press)

@TomKellyGenetics TomKellyGenetics added the enhancement New feature or request label Oct 24, 2022
@TomKellyGenetics TomKellyGenetics self-assigned this Oct 24, 2022
@TomKellyGenetics TomKellyGenetics mentioned this issue Dec 6, 2022
9 tasks
@TomKellyGenetics
Copy link
Member Author

Update: the module running UniverSC v1.2.5.1 is stable so I think it is ready to proceed with developing a subworkflow to run it for scRNA-Seq as discussed with @apeltzer.

@TomKellyGenetics
Copy link
Member Author

I'll post further updates in the PR: #185

@grst grst added this to scrnaseq Feb 21, 2023
@github-project-automation github-project-automation bot moved this to Todo in scrnaseq Feb 21, 2023
@grst grst changed the title Migrate from Cell Ranger to UniverSC to support other technologies Add UniverSC aligner to support other technologies Feb 21, 2023
@github-project-automation github-project-automation bot moved this from Todo to Done in scrnaseq Mar 7, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
Status: Done
Development

No branches or pull requests

1 participant