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Updated: Jun 13, 2026
06:24
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
Chromap Suite: an open-source single-binary platform for agentic multiomic RNA + ATAC profiling
Ling-Hong Hung1, Ka Yee Yeung1
1University of Washington Tacoma.
Biorxiv : the Preprint Server for Biology
|June 12, 2026
Summary
Chromap Suite offers an open-source alternative for multiomic analysis, significantly improving speed and reducing memory usage compared to proprietary tools. This freely redistributable pipeline supports both researchers and AI agents for enhanced biological insights.
Area of Science:
- Computational Biology
- Genomics
- Bioinformatics
Background:
- Single-cell multiomic profiling is crucial for understanding cellular regulatory states.
- Existing analysis toolchains for multiomics, like Cell Ranger ARC, have limitations including proprietary software, restrictive licenses, and non-standard peak calling methods.
- Integrating open-source tools like Chromap and MACS3 has been challenging due to incompatible runtimes.
Purpose of the Study:
- To develop a fully open-source, permissively licensed alternative for multiomic analysis.
- To create a unified pipeline that integrates RNA and ATAC modalities using community-standard methods.
- To provide a user-friendly platform for both human researchers and AI agents.
Main Methods:
- Extended Chromap with native BAM output, in-process narrow peak calling, and support for various input formats.
- Reimplemented MACS3's narrow peak caller in C++ (libMACS3) to eliminate Python dependencies.
- Integrated libchromap and libMACS3 into STAR Suite for concurrent RNA and ATAC analysis in a single binary.
- Developed a Model Context Protocol (MCP) server and browser-based Launchpad for AI and human-driven analysis.
Main Results:
- Achieved a 2.12x speedup and 1.8x reduction in peak memory usage compared to Cell Ranger ARC on a 3K PBMC Multiome dataset.
- The Chromap Suite platform completed analysis in 18 minutes 55 seconds with 44.6 GB peak resident memory.
- Generated byte-identical MACS3 narrow peaks, ensuring compatibility with downstream ATAC analyses.
- The integrated STAR Suite enables concurrent alignment, peak calling, and cell calling for both RNA and ATAC data.
Conclusions:
- Chromap Suite provides a unified, freely redistributable multiomic pipeline that is faster and more memory-efficient than proprietary alternatives.
- The platform's open-source nature and MIT/BSD-3 licenses remove redistribution restrictions.
- The MCP server and Launchpad facilitate straightforward operation by both researchers and AI agents.
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