Getting started
Overview
The tools:
kallisto: Maps RNA-seq reads to a reference transcriptome and stores the results in a BUS file.
bustools: Processes the results in the BUS file to correct barcodes, deduplicate UMIs, and generate quantification files (e.g. count matrices).
kb-python: A wrapper around kallisto and bustools that facilitates usage of those tools and facilitates the generation of a reference transcriptome. The kallisto and bustools binaries come packaged in kb-python.
Installation
Installing kb-python
To install the latest version of the software, which should be sufficient for most purposes, all you have to do is run the following:
pip install kb_python
If you need to install a specific version of kb-python, you can specify the version in the pip install. For example, for version 0.28.2 of kb-python:
pip install kb_python==0.28.2
See also
If you want to install kallisto and bustools from source, please visit the section Installing from source
Usage
There are two main kb-python commands that cover most use cases: kb ref
and kb count
, for building an index from a transcriptome reference and mapping/quantifying sequencing reads, respectively.
To run those commands, you can just type them into the command-line after install kb-python:
kb ref ...
kb count ...
Replace … with whatever parameters you wish to supply to those commands.