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

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

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Single-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.

Original languageEnglish
Article number109
JournalGenome Biology
Issue number1
StatePublished - Dec 2024


  • Donor deconvolution
  • Genetic
  • Hashing
  • Nextflow
  • Single-cell


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