kallisto | bustools

The kallisto, bustools, and kb-python programs are free, open-source software tools that are used together to perform RNA-seq quantification.

Note

This is unofficial documentation that is under active development.

A paper describing the protocols is available as follows:

• Protocols Manual

• Supplementary Manual

Introduction:

• Getting started
  • Overview
  • Installation
  • Usage

Information:

• Installing from source
• Frequently asked questions

Citation:

Melsted P*, Booeshaghi AS*, Liu L, Gao F, Lu Lambda, Min KH, da Veiga Beltrame E, Hjörleifsson KE, Gehring J, Pachter L. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nature Biotechnology 39, 813–818 (2021). https://doi.org/10.1038/s41587-021-00870-2

Melsted P*, Ntranos V*, Pachter L*. The barcode, UMI, set format and BUStools. Bioinformatics 35(11), 4472–4473 (2019). https://doi.org/10.1093/bioinformatics/btz279

Bray N, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 34, 525–527 (2016). https://doi.org/10.1038/nbt.3519