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Add UniverSC aligner to support other technologies #170

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TomKellyGenetics opened this issue Oct 24, 2022 · 2 comments
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Add UniverSC aligner to support other technologies #170

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

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

@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
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