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Workflow library

Browse the verified analysis workflows available in ElemBio Cloud.

Workflows are cloud-hosted pipelines that process system data for analysis, file conversion, and other post-run activities. Element Biosciences and its partners develop and verify each workflow, so you can launch one without building a pipeline yourself.

To run a workflow on new data automatically or on demand, set up an analysis flow. Each time a flow runs, it produces an execution that records the parameters, status, and outputs.

End-to-end data flow in ElemBio Cloud

End-to-end sequencing data flow in ElemBio Cloud.

Available workflows

Each card summarizes one workflow. Assignment workflows carry a blue badge and secondary analysis workflows carry a pink badge. Basic assignment workflows are included with any ElemBio Catalyst subscription. Secondary analysis workflows for sequencing require the premium add-on.

Sequencing

Bases2Fastq

Demultiplexes sequencing run data to generate FASTQ files and a QC report.

Germline secondary analysis with Sentieon

Aligns reads with BWA-mem and calls variants with Sentieon DNAscope. Parameters are pre-set for WGS or enrichment, including hosted BED files.

Germline secondary analysis with NVIDIA Parabricks

Uses GPU-accelerated NVIDIA Parabricks to align reads with BWA-mem and call variants with Google DeepVariant. Parameters are pre-set for WGS or enrichment, including hosted BED files.

Multiomics analysis

Cells2Stats

Generates cell statistics from cell screening run data and prepares output for CytoCanvas™ visualization.

Cell screening secondary analysis

Segments cells, demultiplexes base calls, aligns and assigns 3' untargeted reads, and builds the Spatial Data Object. On ElemBio Catalyst™, the Cytos Cell Screening analysis workflow launches automatically when a Multimodal Pooled Screening run completes.

See also

End-to-end data flow in ElemBio Cloud
Available workflows
- Sequencing
- Multiomics analysis
See also