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 (https://linnarssonlab.org/loompy/kallisto/index.html)
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.
Visit the Getting Started tutorial on Google Colab.
- User documentation and tutorials are available here.
- Developer documentation is hosted on Read the Docs.