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Introduction

kallisto and bustools are wrapped in an easy-to-use program called kb which is part of the kb-python package, and that can be installed on any machine by typing pip install kb-python on the command line. This installs everything needed to process single-cell RNA-seq reads with two simple commands. The first is kb ref and the second kb count:

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$ kb ref -i transcriptome.idx -g transcripts_to_genes.txt -f1 cdna.fa dna.primary_assembly.fa.gz gtf.gz
$ kb count -i index.idx -g t2g.txt -x 10xv2 --h5ad -t 2 read_1.fastq.gz read_2.fastq.gz

For an in-depth overview of kb see the docs.

kallisto and bustools

kb-python utilizes the kallisto and bustools programs. Details on the use of these tools can be found below:

The kallisto manual is available at: https://pachterlab.github.io/kallisto/download

The bustools manual is available at: https://bustools.github.io/manual