kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.
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.
Pubmed ID: 38045414 RIS Download
Research resources used in this publication
None foundAdditional research tools detected in this publication
Antibodies used in this publication
None foundAssociated grants
- Agency: NIGMS NIH HHS, United States
Id: T32 GM008042 - Agency: NIMH NIH HHS, United States
Id: U19 MH114830 - Agency: NHGRI NIH HHS, United States
Id: UM1 HG012077
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This is a list of tools and resources that we have found mentioned in this publication.
Bustools (tool)
RRID:SCR_018210
Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.
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RRID:SCR_018213
Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).
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