Open-MSSPE-Design

Open-MSSPE-Design is a Rust-based pipeline for designing primers for Metagenomic Sequencing with Spiked Primer Enrichment (MSSPE). This approach supports viral diagnostics and genomic surveillance by enriching viral sequences during sequencing, as described in Deng et al. (2020), and openly implemented in nf-msspe by Simon Maestri. This implementation introduces significant revisions to optimize and automate the primer design process.

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Overview

Key features:

• Fully automated primer design workflow.
• Rust implementation for performance and reliability.
• Enhanced filtering for di-nucleotide repeats, homopolymers, and potential secondary structures via deltaG calculations.

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Getting Started

Prerequisites

• Rust (latest stable version)
• Cargo (Rust package manager)
• mafft for multiple sequence alignment
• ntthal from Primer3 package

Installation

Clone the repository and navigate to the project directory:

git clone https://github.com/opendream/open-msspe-design.git
cd open-msspe-design

Install dependecies:

brew install rust
brew install mafft

Input Requirements

Prepare a FASTA file containing viral genome sequences. This will serve as the input for primer design.

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Usage

Build the pipeline:

cargo build --release

To run the pipeline:

./target/release/od-msspe

OR

cargo run

Options

• --input: Path to the input FASTA file containing viral genome sequences.
• --output: Directory where the designed primers will be saved.
• --config: (Optional) Path to a configuration file for advanced settings.

Example

cargo run -- --input data/viral_genomes.fasta --output results/msspe_primers.csv

Debugging

RUST_LOG=info cargo run -- --input data/viral_genomes.fasta --output results/msspe_primers.csv

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Contributions

Contributions, issues, and feature requests are welcome! Please open an issue or submit a pull request to improve the project.

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License

This project is licensed under the MIT License.