Template Switch Aligner

Binary:
Library:

Align two genomic sequences while allowing for template switches.

Installation

Via Cargo (Preferred)

1. Install the rust toolchain by going to rustup.rs and following the instructions. Don't worry, on unix-like systems there is just a single command to execute.

2. Run cargo install tsalign.

3. You can now run tsalign on your command line from anywhere.

If you ever want to update to a new release, simply run cargo install tsalign again.

From Source (For Developers)

1. Install the rust toolchain by going to rustup.rs and following the instructions. Don't worry, on unix-like systems there will just be a single command to be executed.

2. Clone this git repository using git clone <url of this repository>.

3. From within the root of the git repository, you can run cargo run --release -- <arguments> to run tsalign, where <arguments> are the arguments that are passed to tsalign.

Cargo acts as a wrapper here, ensuring that whenever you make changes to the code, it will be recompiled if necessary. Hence, for updating, it is enough to do a git pull.

Usage

Run the installed tool with --help (e.g. tsalign --help if installed via cargo) to get an overview of the available options.