RAPID SINGLE-CELL MULTIOMICS PROCESSING USING AN EXECUTABLE FILE

This disclosure describes methods, non-transitory-computer readable media, and systems that can use a single executable file to run a single-cell multiomics analysis that (i) aligns multiomics reads with a reference genome and (ii) jointly filters cellular barcode sequences for cells based on feature-specific, single-cell read counts. To run such an assay, the disclosed systems identify transcriptomic reads and genomic reads for a sample, where such reads comprise different sets of cellular barcode sequences. In some cases, the disclosed systems further use separate invocations of a configurable processor to align the transcriptomic reads and genomics reads with a reference genome. Based on single-cell counts of aligned transcriptomic reads and aligned genomic reads for target nucleotide sequences, the disclosed systems select a subset of candidate cells corresponding to a subset of cellular barcode sequences. The disclosed systems further generate, for the sample, single-cell multiomics outputs based on the counts of aligned reads.