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VaxPress
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Codon Optimizer for mRNA Vaccine Design
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VaxPress
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# VaxPress VaxPress is a codon optimizer platform tailored for mRNA vaccine development. It refines coding sequences starting from protein or RNA sequences to boost both storage stability and *in vivo* protein expression. Plus, additional properties can be easily programmed into the optimization process with just a few lines of code via a pluggable interface. For the detailed information about VaxPress, including its options and algorithmic features, please refer to the [VaxPress documentation page](https://vaxpress.readthedocs.io/). # Installation ### pip You can install VaxPress via pip. #### Installing ```bash # Create a virtual environment for VaxPress python -m venv /path/to/vaxpress-env # Activate the virtual environment source /path/to/vaxpress-env/bin/activate # Install VaxPress alone pip install vaxpress # Alternatively, install VaxPress with LinearFold (only for non-commercial uses) pip install 'vaxpress[nonfree]' ``` #### Running ```bash # Activate the virtual environment source /path/to/vaxpress-env/bin/activate # Run VaxPress vaxpress -h ``` #### iCodon Dependency If you wish to activate the iCodon predicted stability (`--iCodon-weight`) in the fitness function, ensure you have working installations of *R,* *rpy2* (version >= 3.0) and *iCodon.* For detailed installation instructions, visit [iCodon's GitHub page](https://github.com/santiago1234/iCodon/). ### Conda Alternatively, you may also install VaxPress via a conda package: #### Installation ```bash conda create -n vaxpress -y -c changlabsnu -c bioconda -c conda-forge vaxpress ``` #### Running ```bash # Activate the environment conda activate vaxpress # Run VaxPress vaxpress -h ``` ### Singularity To run VaxPress via Singularity, you will need to install the [Singularity CE](https://sylabs.io/singularity/) first. Download the container image from [the GitHub project page](https://github.com/ChangLabSNU/VaxPress/releases) and place it in a directory of your choice. ```bash singularity run vaxpress.sif -h ``` When using the Singularity image, both the input and output must be somewhere inside your home directory for VaxPress to run without complicated directory binding configurations for Singularity. # Usage ## Quick Start Here's a basic command-line instruction to start using VaxPress. Note that `-i` and `-o` options are mandatory: ```bash vaxpress -i spike.fa -o output --iterations 1000 -p 32 ``` ### Input VaxPress requires a FASTA format input file that contains the CDS (CoDing Sequence) to be optimized. In case the FASTA file holds a protein sequence, the additional `--protein` switch is required. ### Number of Iterations The `--iterations` option is set to `10` by default. However, for thorough optimization, it's recommended to use at least `500` iterations. The optimal number of iterations may differ depending on the length, composition of the input, and the selected optimization settings. It's important to note that the optimization process may stop before completing all the specified iterations if no progress is observed over several consecutive cycles. Guidelines for setting the appropriate number of iterations and other optimization parameters can be found in the [Tuning Optimization Parameters](https://vaxpress.readthedocs.io/en/latest/user_guides.html#tuning-parameters) section. You can set `--iterations` to `0` to generate VaxPress's sequence evaluation report without any optimization. ### Multi-Core Support You can use multiple CPU cores for optimization with the `-p` or `--processes` option. ### More About Options VaxPress offers the flexibility to adjust optimization strategies in detail and integrate with LinearDesign. It also allows several more convenient functions such as preset parameters, user-defined custom scoring functions, and etc. For comprehensive explanation, please refer to [the manual](https://vaxpress.readthedocs.io/en/latest/). ## Output Once you've run VaxPress, the specified output directory will contain the following five files: - ``report.html``: A summary report detailing the result and optimization process. - ``best-sequence.fasta``: The refined coding sequence. - ``checkpoints.tsv``: The best sequences and the evaluation results at each iteration. - ``log.txt``: Contains the logs that were displayed in the console. - ``parameters.json``: Contains the parameters employed for the optimization. This file can be feeded to VaxPress with the `--preset` option to duplicate the set-up for other sequence. # Citing VaxPress If you employed our software in your research, please kindly reference our publication: Ju, Ku, and Chang (2023) Title. Journal. Volume. (in preparation) # License VaxPress is distributed under the terms of the [MIT License](LICENSE.txt). LinearFold and LinearDesign are licensed for non-commercial use only. If considering commercial use, be cautious about using options such as `--lineardesign` and `--folding-engine linearfold`.
