wetSpring
Microbiology and metagenomics
Microbiology and metagenomics — sovereign 16S pipeline (FASTQ→DADA2→taxonomy→UniFrac), 63/63 papers reproduced, 1 runtime dependency (flate2). Replaces Galaxy/QIIME2.
169,944lines of Rust
2,083test functions
724files
3crates
Capabilities
| Category | Primitives |
|---|---|
| 16S Pipeline | FASTQ→quality→merge→dereplicate→DADA2→chimera→taxonomy→diversity→UniFrac — all Rust |
| Chemistry | LC-MS feature extraction, PFAS screening, mzML parsing |
| GPU | 1,077x spectral cosine speedup, 79 barraCuda primitives consumed, zero local WGSL |
| Papers | 63/63 reproduced — Waters c-di-GMP, Liu genomics, deep-sea metagenomics, Jones PFAS |
Composes Into
ToadStool validation (79 primitives consumed, found log_f64 bug), biomeOS, NestGate (NCBI)