A rust implementation of a novel de novo clustering algorithm. isONclust3 is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene family. Output is a tsv file with each read assigned to a cluster-ID and a folder 'fastq' containing one fastq file per cluster generated. Detailed information is available in paper.
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 clone https://github.com/aljpetri/isONclust3.git use the following two commands to compile the code:
cd isONclust3
cargo build --release ( Compile the current package, the executable is then located in target/release)
To run the algorithm:
If you encounter any problems, please raise an issue on the issues page, you can also contact the developer of this repository via: alexander.petri[at]math.su.se