About

multiome-wf is a Snakemake workflow for common single cell sequencing analyses.

With the advent of new sequencing methods and associated data sets, combining different single cell sequencing modalities is cumbersome and error-prone. A core feature of the multiome-wf is standardizing how disparate data types are combined and preprocessed prior to downstream analyses.

The workflow was built around 10X Genomics products, but should work with any single cell data set as long as the input matrices have been properly formatted.

Some of the modalities this workflow supports include:

  • Gene Expression: mapped and quantified by cellranger count and cellranger aggr

  • ATAC: mapped and quantified by cellranger-atac count and cellranger-atac aggr

  • Multiome (Gene Exression + ATAC from same cell), CITE-Seq: mapped and quantified by cellranger-arc count and cellranger-arc aggr

  • Cell Multiplexing (Cell Multiplexing Oligos): demultiplexed using cellranger pipelines.

  • Multiple Batches, Multiple experimental conditions

Note

  • While this workflow does some basic tertiary analyses, such as differential testing, the core purpose of this workflow is preparing a unified dataset to be used as input for standalone downstream analyses, such as Trajectory Inference, Gene-Peak Interactions, etc which are not currently supported by this workflow.

  • Users need familarity with Snakemake, Conda, and Seurat for effective use of multiome-wf.

Getting Started

See Setting up a project to get started.

See Overview of workflows to learn more about the supported workflows.