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bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.

The design and motivation for the BUS format and BUStools are described in detail in

P Melsted, V Ntranos, L Pachter, The Barcode, UMI, Set format and BUStools, bioRxiv 2018 pp: 472571.

BUS format

bustools works with BUS files which can be generated efficiently from raw sequencing data, e.g. using kallisto.


Download bustools with

git clone

Move to the bustools directory

cd bustools

Make a build directory and move there:

mkdir build

cd build

Run cmake:

cmake ..

Build the code:


The bustools executable is now located in build/src. To install bustools into the cmake install prefix path type:

make install


To see a list of available commands type bustools in the terminal

> bustools 
Usage: bustools <CMD> [arguments] ..

Where <CMD> can be one of:

sort            Sort bus file by barcodes and UMI
text            Output as tab separated text file

Running bustools <CMD> without arguments prints usage information for <CMD>


Raw BUS output from pseudoalignment programs may be unsorted. To simply and accelerate downstream processing BUS files can be sorted using bustools sort

> bustools sort 
Usage: bustools sort [options] bus-files

-t, --threads         Number of threads to use
-o, --output          File for sorted output

This will create a new BUS file where the BUS records are sorted by barcode first, UMI second, and equivalence class third.


BUS files can be converted to a tab-separated format for easy inspection and processing using shell scripts or high level languages. bustools text

> bustools text
Usage: bustools text [options] bus-files

-o, --output          File for text output