cyto is an ultra-high throughput processor for 10x Genomics Flex single-cell sequencing that achieves a 16.5-fold speedup over CellRanger through direct k-mer lookup and novel binary formats (IBU and BINSEQ) optimized for parallel processing. By exploiting the fixed sequence geometry of Flex libraries rather than using alignment-based mapping, cyto processes a 320,000-cell dataset in 13 minutes while using 2.4-fold less memory and performing 5.6-fold less disk I/O, maintaining 99.85% concordance with CellRanger outputs. This computational efficiency enables cost-effective processing on smaller cloud instances and makes atlas-scale single-cell projects and genome-wide perturbation screens computationally feasible.
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