BioTools-Dev
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GenoScanner
GenoScanner PublicExperimental tool to taxonomically classify microbial genomes in a few minutes
Shell 1
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rapdtool-benchmark
rapdtool-benchmark PublicReproducible benchmark kit for RaPDTool — type-material–anchored, genome-resolved metagenomics vs Kraken2 and MetaPhlAn4. Scripts, curated inputs, gold standards, summary results and figures to reg…
Python
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mash_boundaries
mash_boundaries PublicWe establish strict, actionable thresholds: species at d ≤ 0.043 and genus at 0.043 < d ≤ 0.13. These measurements demonstrate that current standards are fundamentally flawed. The ubiquitous conver…
Python
Repositories
- rapdtool-benchmark Public
Reproducible benchmark kit for RaPDTool — type-material–anchored, genome-resolved metagenomics vs Kraken2 and MetaPhlAn4. Scripts, curated inputs, gold standards, summary results and figures to regenerate every number in the paper.
- mash_boundaries Public
We establish strict, actionable thresholds: species at d ≤ 0.043 and genus at 0.043 < d ≤ 0.13. These measurements demonstrate that current standards are fundamentally flawed. The ubiquitous conversion of distance to identity as 1 − d is systematically biased, overstating relatedness by 12d points. We correct this with an exact formulation
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