kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq

RNA-seq preprocessing must convert raw reads into expression measurements for bulk, single-cell, and single-nucleus assays. The workflow must coordinate reference generation, mapping, quantification, and assay-specific read structures. kb-python reduces kallisto-bustools preprocessing to kb ref and kb count while supporting bulk, single-cell, single-nucleus, and joint nascent/mature-RNA analyses.