Hi everyone! Do we have a pipeline in nf-core coll...
# meta-omicso
Olga Brovkina
08/21/2025, 7:21 AMHi everyone! Do we have a pipeline in nf-core collection which captures spatial metatranscriptomics?
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James Fellows Yates
08/21/2025, 7:23 AMNo but that sounds awesome
James Fellows Yates
08/21/2025, 7:23 AM😱
James Fellows Yates
08/21/2025, 7:23 AMJames Fellows Yates
08/21/2025, 7:23 AMThose are the existing spatial pipelines...
James Fellows Yates
08/21/2025, 7:23 AMyou mightwant to check each one if they support the 'meta-' bit
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Olga Brovkina
08/21/2025, 7:31 AMOk, it seems, that there is no particular pipeline. I thought Microcart (https://www.nature.com/articles/s41467-025-56237-7) were implemented in one of the spatial pipelines, but unfortunately not.
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James Fellows Yates
08/21/2025, 7:32 AMimage.png
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Olga Brovkina
08/21/2025, 7:35 AMI will talk with Florian Heyl, the have a collection of spatial pipelines, probably we can collaborate
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Daniel Lundin
08/21/2025, 9:10 AMSounds interesting. Since I work on #C01U1E95JQ5 and #C02FC6VFQG1, both for metatranscriptomes, I get curious what the approach would be: de novo assembly or mapping -- or something else?
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Olga Brovkina
08/21/2025, 11:12 AMI probably put the initial question wrong. I was thinking of the type of data used in the recent MicroCart paper — i.e. spatial transcriptomics on tissue (GeoMx, Visium, etc.) combined with microbial 16S/spatial probes. Not classical metatranscriptomics (assembly or mapping).
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Daniel Lundin
08/21/2025, 11:16 AMI see. I don't know much about these things, so I was just curious. Sounds like a new pipeline though.
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