Discussion: other formats worth supporting in `adata convert`

[Claptar]

Part of #20.

Candidates beyond the first round. Please 👍 or comment with the ones you actually run into (and example files, if you can share them).

Pipeline outputs

• STARsolo full Solo.out (Gene / GeneFull / Velocyto / SJ) → one AnnData with layers — partly covered by Convert: MTX and 10x MTX folders, import and export (streaming) #24
• alevin-fry USA mode (quants_mat.mtx + spliced/unspliced/ambiguous → layers)
• kallisto | bustools (kb count mtx / loom / h5ad outputs)
• 10x Multiome / ATAC filtered_peak_bc_matrix.h5 — Convert: 10x HDF5 (Cell Ranger *_feature_bc_matrix.h5), import and export #23 with the Peaks feature type
• Space Ranger / Visium and Xenium cell_feature_matrix.h5 + cells.parquet / spatial/ — matrix via Convert: 10x HDF5 (Cell Ranger *_feature_bc_matrix.h5), import and export #23, coordinates → obsm["spatial"]

Container formats

• MuData .h5mu — extract a modality (/mod/<name> is an embedded AnnData) or merge several into one. Current SCENIC+ writes this.

R ecosystem

• Seurat .h5Seurat (SeuratDisk, plain HDF5 — readable with h5py), both directions
• SingleCellExperiment via HDF5Array / zellkonverter .h5
• .rds is out of scope (not HDF5, needs R)

Other

BPCells directories, UMI-tools count tables, .soft.gz (GEO), Excel.