Practical Omnitigs

This is a repository to conduct experiments with omnitig-related models in the context of genome assembly. The algorithms are implemented in Rust, and around that we built a snakemake toolchain to conduct experiments. To ensure reproducibility, we wrapped everything into a conda environment.

Usage

Required Software

• conda >= 4.8.3 (lower might be possible, but has not been tested)

Setup

First, set up the conda environment of this project.

conda env create -f environment.yml

Then, activate the environment.

source activate practical-omnitigs

Running Experiments

Make sure that you are in the right conda environment (should be practical-omnitigs).

conda info

Subsequently, experiments can be run using snakemake.

snakemake --cores all <experiment>

Valid experiments are:

• selftest: Check if you have conda set up correctly. It prints the version of snakemake conda and wget. The versions of snakemake and conda should match the definition in /environment.yaml and the version of wget should match the definition in /config/conda-selftest-env.yaml.
• test: execute all integration tests of this project on a single small sample genome.
• test_all: execute all integration tests of this project on all defined genomes (potentially very large).

The experiments are run inside a conda environment that is set up by snakemake. This ensures reproducibility of the results and automates the installation of required tools.

Using the Implementation Directly

The Rust code written for this project includes a command line interface that can be used directly. For documentation on how to use it, please refer to the documentation of the cli crate.

Troubleshooting

If you have problems with using this software package, take a look at our troubleshooting page. If that does not solve your issue, do not hesitate to file a bug report.

Technical Information

Directory Structure

• .github: GitHub workflows for continuous testing.
• .idea: Configuration for the IntelliJ IDEA integrated development environment.
• config: All config files related to the experiments, including conda environments and experiment declarations.
• data: Data used and produced by the experiments.
• external-software: Location to install external software required by the experiment pipeline.
• implementation: The algorithms that we are testing. Everything is written in Rust.

Implementation

The algorithms of this project are implemented in Rust. We split the implementation into multiple library crates to increase the reusability of our code. On top of that, the cli crate provides all implemented functionality via a command line interface. Refer to its documentation for more information.

Except for cli, all crates are published on crates.io.

License

This project is licensed under the terms of the BSD 2-Clause license. See LICENSE.md for more information.

How to Cite

If you use this code in your research project, please cite it as "Safe and Complete Genome Assembly in Practice, DOI: 10.5281/zenodo.4335367"