hadge: a comprehensive pipeline for donor deconvolution in single-cell studies

Author:

Curion Fabiola,Wu Xichen,Heumos Lukas,André Mylene Mariana Gonzales,Halle Lennard,Ozols Matiss,Grant-Peters Melissa,Rich-Griffin Charlotte,Yeung Hing-Yuen,Dendrou Calliope A.,Schiller Herbert B.,Theis Fabian J.ORCID

Abstract

AbstractSingle-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue.

Funder

Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)

Publisher

Springer Science and Business Media LLC

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