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bioRxiv · 10.1101/2020.11.18.389189

Efficient and precise single-cell reference atlas mapping with Symphony

Kang, J. B.·Nathan, A.·Millard, N.·Rumker, L.·Moody, D. B.·Korsunsky, I.·Raychaudhuri, S.
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Abstract

Recent advances in single-cell technologies and integration algorithms make it possible to construct comprehensive reference atlases encompassing many donors, studies, disease states, and sequencing platforms. Much like mapping sequencing reads to a reference genome, it is essential to be able to map query cells onto complex, multimillion-cell reference atlases to rapidly identify relevant cell states and phenotypes. We present Symphony (https://github.com/immunogenomics/symphony), an algorithm for building integrated reference atlases of millions of cells in a convenient, portable format that enables efficient query mapping within seconds. Symphony localizes query cells within a stable low-dimensional reference embedding, facilitating reproducible downstream transfer of reference-defined annotations to the query. We demonstrate the power of Symphony by (1) mapping a multi-donor, multi-species query to predict pancreatic cell types, (2) localizing query cells along a developmental trajectory of human fetal liver hematopoiesis, and (3) inferring surface protein expression with a multimodal CITE-seq atlas of memory T cells.

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Kang, J. B., Nathan, A., Millard, N., Rumker, L., Moody, D. B., Korsunsky, I., Raychaudhuri, S.. 2020-11-20. Efficient and precise single-cell reference atlas mapping with Symphony. https://doi.org/10.1101/2020.11.18.389189

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