auto-optimize makes bedtools intersect 3-5x faster with 20x less memory, output unchanged
jmschreiber91 · x · 2026-10-30
jmschrei (Programmable Genomics Lab, UMass Chan) shows auto-optimize results on classic bioinformatics tools: Picard MarkDuplicates 2-9x faster; bedtools intersect 3x faster with a third of the memory. The GitHub PR details how it changes how bedtools reads, stores, indexes and prints interval records: unsorted intersect 3-5x faster, subtract/fisher/map/merge/jaccard/coverage/closest 1.1-1.7x faster, peak memory up to 20x lower, with every output byte unchanged. Benchmarks: an intersect over 5.7M RepeatMasker records drops from 11.44s to 2.39s, peak memory from 2,922MB to 550MB; faster in 9/9 paired comparisons (median -8.66s, p=0.0039). An opt-in FAST=1 build with -O3, LTO and PGO reaches 1.98s.
Related event: AI auto-optimize tool speeds up classic bioinformatics tools up to 10x(3 posts)→
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