Python wrapper around kallisto | bustools for scRNA-seq analysis
kb-python is a python package that wraps the kallisto | bustools single-cell RNA-seq workflow . It was developed by Kyung Hoi (Joseph) Min and A. Sina Booeshaghi.
The wrapper simplifies downloading and running of the kallisto
 and bustools  programs. It was inspired by Sten Linnarsson’s
loompy fromfq command (http://linnarssonlab.org/loompy/kallisto/index.html)
kb program consists of two parts:
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
kallisto index .
kb count command runs the kallisto  and bustools  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:
 Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature biotechnology, 34(5), 525.
 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 page.
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