Скачать или смотреть cyto: ultra-high throughput processing of 10x-flex single cell sequencing

Arc Bioinformatics Scientist Noam Teyssier presents cyto, 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.

Link to preprint: https://www.biorxiv.org/content/10.64...

Citation:
Teyssier, N., & Dobin, A. (2026) cyto: ultra-high throughput processing of 10x-flex single cell sequencing. BioRxiv. https://doi.org/10.64898/2026.01.21.7...