GAMBA is a tool coded in Rust that identifies polycistronic transcriptional units (operons) among the annotated transcripts of a GTF file. The detection is based on transcript position, structure and expression level. It requires a GTF files with the values of 'cov' and 'fpkm', used during operon selection.
Source and binary files can be directly downloaded from the Releases page on this repository. Other option is to clone the repository and build the binary with cargo:
git clone https://github.com/nurie05/gamba-tool.git
cd gamba-tool
cargo build --release
target/release/gamba --help
Additionally it is possible to install it by using Homebrew:
brew tap nurie05/homebrew-tools
brew install nurie05/homebrew-tools/gamba
This tool has few parameters that can be specified (use --help to get the usage message):
-f, --file <FILE> Path to the input GTF file
-t, --threshold <THRESHOLD> Coverage threshold multiplier [default: 1]
-m, --min-overlap <MIN_OVERLAP> Minimum percentage of exonic overlap to be considered 'contained transcript' [default: 0.5]
-b, --bp-overlap <BP_OVERLAP> Minimum bp overlap to consider exonic overlap [default: 50]
-p, --prefix <PREFIX> Output file prefix
-o, --outdir <OUTDIR> Output directory
--log <LOG> Log file path
-h, --help Print help
-V, --version Print version
The generic command line for the default usage is:
gamba --file FILE.gtf --threshold 1 --output OUTDIR -p FILE-PREFIX --log FILE-PREFIX_gamba.log
Notice that only the '--file' parameter is mandatory. In case '--output' is not specified, it will output all the files in the same directory where the GTF file is. In case '--prefix' is not specified, it will use the file name as output prefix for all files, including the log file.
If you use GAMBA in your research, please cite the following publication:
- NTorres-Aguila, N.P., Cassà, B., and Canestro, C. (2025). CORAL: Accurate annotation of compact genomes using long-read RNA-seq, demonstrated in Oikopleura dioica. bioRxiv. DOI: 10.64898/2025.12.04.692336