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

Delaney K Sullivan; Kyung Hoi Joseph Min; Kristján Eldjárn Hjörleifsson; Laura Luebbert; Guillaume Holley; Lambda Moses; Johan Gustafsson; Nicolas L Bray; Harold Pimentel; A Sina Booeshaghi; Páll Melsted; Lior Pachter

doi:10.1101/2023.11.21.568164

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

bioRxiv [Preprint]. 2024 Jan 23:2023.11.21.568164. doi: 10.1101/2023.11.21.568164.

Authors

Delaney K Sullivan^{1

2}, Kyung Hoi Joseph Min³, Kristján Eldjárn Hjörleifsson⁴, Laura Luebbert¹, Guillaume Holley⁵, Lambda Moses¹, Johan Gustafsson⁶, Nicolas L Bray⁶, Harold Pimentel^{7

8

9}, A Sina Booeshaghi^{1

10}, Páll Melsted^{5

10}, Lior Pachter^{1

4}

Affiliations

¹ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
² UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
³ Ginkgo Bioworks, Boston, MA, 02210, USA.
⁴ Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
⁵ deCODE Genetics/Amgen Inc., Reykjavik, Iceland.
⁶ Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
⁷ Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
⁸ Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
⁹ Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
¹⁰ School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.

Abstract

The term "RNA-seq" refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples, or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data.

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Preprint

Abstract

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