Single cell multiplexing techniques (cell hashing and genetic multiplexing) allow to combine multiple samples, thereby optimizing sample processing and reducing batch effects. 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 developed hadge ( ha shing d econvolution combined with ge notype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining the best performing methods and we demonstrate how this approach leads to recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue.

hadge: a comprehensive pipeline for donor deconvolution in single cell