Feature request: Add output mode compatible with Read10X() in Seurat (spliced/unspliced separated as in CellRanger format)

[BenjaminDEMAILLE]

Hi,
Thanks for the amazing work on kb-python. I’d like to request a feature that would improve integration with Seurat and other R-based analysis tools.

Request

Please consider adding an optional output mode that mimics the CellRanger output structure, while separating spliced and unspliced matrices as independent assays of the same sample. Ideally:
• The output folder would contain subfolders like:

output_dir/
  spliced/
    barcodes.tsv.gz
    features.tsv.gz
    matrix.mtx.gz
  unspliced/
    barcodes.tsv.gz
    features.tsv.gz
    matrix.mtx.gz

Motivation

This would restore compatibility with older kb-python workflows and enable smoother integration with Seurat-based pipelines, especially for downstream analyses involving RNA velocity or transcriptional dynamics. Currently, the loom/h5ad outputs require custom handling or Python-to-R conversion steps, which can be error-prone or inconvenient.

A flag like --cellranger-style would be much appreciated!

Thanks again for your work!

[github-actions]

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[Yenaled]

fyi, the bot has closed this issue but it’s still on our radar!