oddSNP documentation¶
Donor multiplexing is a powerful strategy to increase scale, lower the costs, and reduce batch effects in single-cell RNA sequencing (scRNAseq), but clear guidelines for experimental design are lacking, forcing researchers to risk costly demultiplexing failures. To address this, we introduce SNP-Information Content (SNP-IC) and cell-paird SNP-Information Content (cpSNP-IC), quantitative metrics that can be computed from simple, unpooled pilot data and that accurately predict the success of demultiplexing. oddSNP is an open-source framework for computing these metrics, enabling in-silico titration of sequencing depth and donor complexity to optimize experimental design before committing to large-scale studies.
Details on these metrics and the implementation of the tool are available in the manuscript entitled: OddSNP: a predictive framework for optimizing multiplexed single-cell RNA-seq.
oddSNP is developed at the Nemoto-lab, The University of Osaka.
Contents:
How to Cite¶
If you use oddSNP in your research, please cite:
BibTeX¶
@article{osorio2025oddsnp,
title = {OddSNP: a predictive framework for optimizing multiplexed single-cell RNA sequencing},
author = {Allendes Osorio, R.S. and Nishimura, T. and Shigihara, Y. and Kimura, M. and Takebe, T. and Nemoto, T.},
journal = {bioRxiv},
year = {2025},
doi = {10.64898/2025.12.08.692882},
url = {https://www.biorxiv.org/content/10.64898/2025.12.08.692882v1},
note = {Preprint}
}