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.
bustools works with BUS files which can be generated efficiently from raw sequencing data, e.g. using kallisto.
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
Options:
-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
Options:
-o, --output File for text output