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Python wrapper around kallisto | bustools for scRNA-seq analysis

Project description


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kb-python is a python package that wraps the kallisto | bustools single-cell RNA-seq workflow [1]. It was developed by Kyung Hoi (Joseph) Min and A. Sina Booeshaghi.

The wrapper simplifies downloading and running of the kallisto [1] and bustools [2] programs. It was inspired by Sten Linnarsson’s loompy fromfq command (

The kb program consists of two parts:

The kb ref command builds or downloads a species-specific index for pseudoalignment of reads. This command must be run prior to kb count, and it runs the kallisto index [1].

The kb count command runs the kallisto [1] and bustools [2] programs. It can be used for pre-processing of data from a variety of single-cell RNA-seq technologies, and for a number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.). The output can be saved in a variety of formats including mtx and loom.

If you use kb we ask that you cite the following two papers:

[1] Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature biotechnology, 34(5), 525.

[2] Melsted, P., Booeshaghi, A. S., Gao, F., da Veiga Beltrame, E., Lu, L., Hjorleifsson, K. E., Gehring, J., & Pachter, L. (2019). Modular and efficient pre-processing of single-cell RNA-seq. BioRxiv, 673285.


None. The kallisto and bustools binaries are included with the package.

Getting Started

Visit the Getting Started page.


  • User documentation and tutorials are available here.
  • Developer documentation is hosted on Read the Docs.

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