scFlow – a scalable and reproducible analysis pipeline for single-cell RNA sequencing data

Advances in single-cell RNA-sequencing technology over the last decade have enabled exponential increases in throughput: datasets with over a million cells are becoming commonplace. The burgeoning scale of data generation, combined with the proliferation of alternative analysis methods, led researchers at the Imperial College London to develop the scFlow toolkit and the nf-core/scflow pipeline for reproducible, efficient, and scalable analyses of single-cell and single-nuclei RNA-sequencing data. The scFlow toolkit provides a higher level of abstraction on top of popular single-cell packages within an R ecosystem, while the nf-core/scflow Nextflow pipeline is built within the nf-core framework to enable compute infrastructure-independent deployment across all institutions and research facilities. The researchers present their flexible pipeline, which leverages the advantages of containerization and the potential of Cloud computing for easy orchestration and scaling of the analysis of large case/control datasets by even non-expert users. They demonstrate the functionality of the analysis pipeline from sparse-matrix quality control through to insight discovery with examples of analysis of four recently published public datasets and describe the extensibility of scFlow as a modular, open-source tool for single-cell and single nuclei bioinformatic analyses.

Single-cell analysis pipeline with nf-core/scow using the scFlow toolkit


Gene-cell matrices from multi-sample case/control studies are analysed reproducibly across major analytical steps: (a) individual sample quality control including ambient RNA profiling, thresholding, and doublet/multiplet identification, (b) merged quality control including inter-sample quality metrics and sample outlier identification, (c) dataset integration with visualization and quantitative metrics of integration performance, (d) exible dimension reduction with UMAP and/or tSNE, (e) clustering using Leiden/Louvain community detection, (f) automated cell-type annotation with rich cell-type metrics and marker gene characterization, (g) exible differential gene expression for categorical and numerical dependent variables, (h) impacted pathway analysis with multiple methods and databases, and (i) Dirichlet modeling of cell-type composition changes. A high-quality, fully annotated, quality-controlled SingleCell- Experiment (SCE) object is output for additional downstream tertiary analyses. Interactive HTML reports are generated for each analytical step indicated (grey icon). Analyses are efficiently parallelized where relevant (steps a,g,h, and i) and all steps benefit from NextFlow cache enabling parameter tuning with pipeline resume particularly useful for dimension reduction (d) and clustering (e).


Khozoie C, Fancy N, Marjaneh MM, Murphy AE, Matthews PM, Skene N. (2021) scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data. bioRXiv [online preprint]. [abstract]

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