bramble
Project spliced genomic alignments into transcriptomic space, enabling transcript quantification to work with genomic alignments.
bramble works with any alignment method and any quantification method that can use alignments as input, with several modes optimized for different short- and long-read sequencing technologies. It's available as a standalone executable in either C++ or Rust, as a library in Rust, or directly in salmon or oarfish.
Get started
Installation
Build from source with meson, or install the Rust CLI via cargo.
Rust library
bramble-rs is the I/O-free core library used by the CLI, Salmon, and Oarfish.
Getting help
Run bramble --help to see all available options. For issues or
questions, please open an issue
on GitHub, or reach out at zrudnic1@jh.edu.