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Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNAseq data due to their limited scalability. Here we introduce Falco, a cloud-based framework for parallelised processing of large-scale transcriptomic data. The pipeline utilises state-of-the-art big data technology of Apache Hadoop and Apache Spark to perform massively parallel alignment, quality control, anddoi:10.1093/bioinformatics/btw732 pmid:28025200 fatcat:sdazrnj3dnc33hqyosil44hsza