Multiomics workflow
Learn what the multiomics workflow does and how it turns an AVITI24™ cell screening run into a Spatial Data Object.
The multiomics workflow is the Nextflow workflow by Element Biosciences that processes an AVITI24 Cytos™ cell screening run through 3′ alignment and assignment and repackages it into a new Spatial Data Object (SDO). This workflow is necessary for cell screening runs that contain 3′ transcriptome data, such as Cytos 3′ Transcriptome or Cytos Multimodal Pooled Screening. It runs cell segmentation, demultiplexing, 3′ alignment and gene assignment, and SDO assembly as one pipeline, so every sequenced read is linked to a cell and a position.
The workflow is distributed as the Elembio/elembio-multiomics-nf repository on GitHub. On ElemBio Catalyst it launches automatically when a cell screening run completes; see the Cytos Cell Screening analysis workflow page in the Workflow Library. This section covers running it yourself in any Nextflow environment.
How it fits
- The AVITI24 System writes a run directory with base calls, images,
RunParameters.json,RunManifest.csv, andPanel.json. - The multiomics workflow reads that directory and produces an SDO (
{run_id}.zarr.zip), per-stage outputs, and provenance. - The multiomics Python package loads the SDO in Python; CytoCanvas Desktop and CytoCanvas Studio visualize it.
Stages
FASTQ files are routed by assay type as declared in Panel.json. Runs with no 3′ RNA batches skip the alignment stage and still produce an SDO.
| Stage | Description |
|---|---|
| Cells2Stats | Performs cell segmentation, resolves spatial coordinates, and generates per-cell statistics and QC. |
| Bases2Fastq™ | Demultiplexes base calls into FASTQ files per sample, well, and batch. |
| 3′ FASTQ to parquet | Aligns 3′ untargeted reads with STAR, assigns them to genes, and produces cell × gene count matrices. |
| Build SpatialData | Combines spatial data, images, and expression data into one SpatialData .zarr store. |