Universal preprocessing of single-cell genomics data

bioRxiv [Preprint]. 2023 Sep 15:2023.09.14.543267. doi: 10.1101/2023.09.14.543267.


We describe a workflow for preprocessing a wide variety of single-cell genomics data types. The approach is based on parsing of machine-readable seqspec assay specifications to customize inputs for kb-python, which uses kallisto and bustools to catalog reads, error correct barcodes, and count reads. The universal preprocessing method is implemented in the Python package cellatlas that is available for download at: https://github.com/cellatlas/cellatlas/.

Publication types

  • Preprint