figwig benchmarks: 90,543 fiber-seq reads read in 0.42s vs 27s for scipy CSR
jmschreiber91 · x · 2026-10-28
jmschreiber91 shares figwig performance numbers on fiber-seq data: 90,543 genome-wide reads (62 MB, one track per 1,024 reads) write in 6.8s single-threaded, and summing all reads over 8,192 windows takes 0.42s versus 3.8-27s for a scipy CSR layout that needs 12.7 GB in memory. figwig merges multiple experiments into one data structure, yielding far smaller files and much faster readers/writers.
Related event: figwig: A Multidimensional Data Format for Genomic Machine Learning(8 posts)→
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