Tool: spades-rs — a Rust port of SPAdes genome assembler (seeking feedback and benchmarking)
I have written an experimental rewrite/port of the SPAdes genome assembler in Rust: https://github.com/sagnikrout/spades-rs
The goal of this project is to explore whether porting SPAdes components to Rust can improve memory safety, maintainability, and concurrency overhead during graph construction and contig assembly. The codebase was developed with the assistance of LLMs alongside manual verification of the core de Bruijn graph algorithms.
Repository: https://github.com/sagnikrout/spades-rs
I am sharing this with the community to get feedback on:
- Correctness compared to original SPAdes outputs on standard bacterial test datasets.
- Memory usage and runtime performance during k-mer counting and de Bruijn graph compaction.
- Areas where assembly heuristics diverge from SPAdes 3.x behavior.
Contributions, issue reports, or independent benchmark comparisons on standard datasets (e.g., E. coli K-12) are welcome.
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You should list relevant LLMs as co-authors on the GitHub repo to be transparent.
Thanks for the note. I have added an explicit attribution in the repository README stating that Gemini 3.8 Flash was used for drafting and translation assistance, alongside manual verification of the core graph algorithms.