figwig stores 10,246 single-cell ATAC profiles in 1 GB, reads chunks up to 100x faster
jmschreiber91 · x · 2026-10-28
jmschreiber91 shows figwig excels at single-cell data too: 10,246 PBMC ATAC cells genome-wide fit in a 1.0 GB position-ordered figwig file; writing 488M cut sites takes 68s single-threaded (36s at 32 threads); dense reads of 128 cells over 8,192 windows take 0.16s versus 0.26-136s for per-cell bigwig files (1.4 GB total). The trick is merging many experiments into one compact data structure with fast chunked reads into a DataLoader-like object.
Related event: figwig: A Multidimensional Data Format for Genomic Machine Learning(8 posts)→
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