#37 · Tools & infrastructure

Compiled-language rewrites accelerate VCF filtering and variant effect annotation

The dominant thread in this set is throughput engineering for established genomics workflows. vcfilt, a Go streaming VCF filter using zero-allocation byte-scan parsing, reports a 12.2x single-thread speedup over bcftools 1.18 on 1000 Genomes chr20 data. fastVEP reimplements the Ensembl VEP annotation engine in Rust, reports 22-24x speedups over VEP, and annotates GIAB HG002 whole-genome sequencing in 86 s. Both papers address runtime performance of standard per-variant processing rather than the underlying data model. The remaining items do not share this thread. A benchmark of agentic large language models on 73 protein orthogroups reports full coverage and moderate reproducibility alongside persistent biological overinterpretation. A separate preprint proposes a deterministic kernel-like dispatch network encoded in the human proteome and genome using 6-bit encoding, tested with null models and DepMap and STRING data.