At the moment building from source is the only option to install the tool. This requires users to install the Rust programming language onto their system.
You can install rust via
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh (for macOS and Linux or other Unix-based OS). For Windows please follow the instructions on the following site: https://forge.rust-lang.org/infra/other-installation-methods.html .
After cloning the repository via git@github.com:aljpetri/cONcat.git use the following two commands to compile the code:
cd cONcat/cONcat_Code
cargo build --release ( Compile the current package, the executable is then located in target/release)
Please note that cONcat depends on Edlib and, therefore, has dependencies to cmake and g++ .
cONcat --expected Path/to/Expected_fragments.csv --fastq path/to/1.fastq --outfile path/to/outfile --verbose
Please cite this study when using cONcat:
cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads, Alexander J. Petri, Mai Thi-Huyen Nguyen, Anjali Rajwar, Erik Benson, Kristoffer Sahlin LINK.