Omnition Analysis Software

Omnition Analysis Software


The Omnition Analysis Software Version 1.0.0 (ATAC module) is a robust pipeline analysis tool for processing, visualizing, and reporting single-cell ATAC-Seq data produced with the SureCell ATAC-Seq Assay and ddSEQ-generated combinatorial indexing ATAC protocols.  

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Download Omnition Analysis Software

The Omnition Analysis Software Version 1.0.0 (ATAC module) is a pipeline analysis tool that can QC, analyze and report single-cell ATAC-Seq data generated from the Bio-Rad SureCell ATAC-Seq assay and ddSEQ-deployed combinatorial indexing ATAC-Seq protocols as described in Lareau et al. (2019).

Compared to the Bio-Rad ATAC Analysis Toolkit, Omnition Analysis Software offers better usability and functionality as highlighted below: 

  • Streamlined, robust and efficient workflow
  • Enabling batch analysis and reporting for multiple samples
  • Supporting ddSEQ-deployed combinatorial indexing ATAC protocols
  • Open-source, available for download

Applications and Uses

  • Single-cell ATAC-Seq data analysis and reporting
  • Single-cell combinatorial indexing ATAC-Seq data analysis and reporting

How to Run the Omnition

Omnition v1.0.0, the ATAC module, enables QC, analysis and reporting of data generated with the ddSEQ-deployed single-cell ATAC assay and combinatorial indexing ATAC protocols. Watch this tutorial video to learn how to install the Omnition and how to process and report your single-cell ATAC-seq data.


Example Omnition Reports

Data Sets*

  • Dataset 1 — Mouse Brain (46,653 cells): Frozen whole brain tissue from two adult mice, purchased from BrainBits, and processed according to the Omni-ATAC Protocol to isolate nuclei.
  • Dataset 2 — Combinatorial profiling of resting and stimulated bone marrow (136,463 cells): Frozen human bone marrow mononuclear cells from AllCells, stimulated with and without LPS, and barcoded with 96 indexed Tn5 transposases prior to droplet encapsulation.
  • Dataset 3 — Isolated populations from peripheral blood (52,873 cells): Frozen human bone marrow CD34+ stem/progenitor cells, and isolated peripheral blood CD4+ T cells, CD8+ T cells, Monocytes, B cells, and NK cells, bought from AllCells and processed according to the Whole-Cell Protocol provided in the ATAC-Seq User Guide.

*Datasets are from SubSeries that are part of the SuperSeries cited below.

SuperSeries: Lareau CA, Duarte FM, Chew JG, Kartha VK et al. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nat Biotechnol 2019 Aug;37(8):916-924.



Number Description Options
Omnition Analysis Software Report Guide
Omnition Analysis Software User Guide