{
  "id": 7840023,
  "title": "Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis",
  "url": "https://urgent.news/2026/09/16/flow-orchestrated-regulatory-genomics-engine-forge-a-configurable",
  "topic": "science",
  "section": "Science",
  "published": "2026-09-16T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.09.10.750690v1?rss=1"
  },
  "original_language": "en",
  "account": "The regulatory inference from single-nucleus multiome (snMultiome) assays is challenging to scale, audit, and reproduce. The snMultiomics field and its tools lack standardization. To tackle these issues, researchers created FORGE, a customizable Nextflow workflow. FORGE processes paired data, from raw counts and fragments to regulatory network inference, and offers a comprehensive differential testing suite. The workflow is containerized, tracks provenance, is interruption-tolerant, performs well in compute-intensive cluster environments, and allows for detailed customization of specific processes.\n\nFORGE automates the analysis of standalone snRNA-seq and snATAC-seq, integrates the pair using complementary linear and nonlinear latent-variable models, and carries them through regulatory-network inference and differential testing. The researchers tested FORGE on four human and mouse datasets, covering blood, brain, and kidney, as well as two snMultiome chemistries. They also analyzed a twelve-sample CRND8 Alzheimer's disease cohort. FORGE demonstrated cross-modal agreement, missing-modality reconstruction, and accounted for computational cost.\n\nIn the Alzheimer's cohort, FORGE identified a glial Mef2c-associated program. In human peripheral blood mononuclear cells, FORGE combined evidence models that largely supported previously published regulatory links and proposed an additional CD83 myeloid module.",
  "summary": "MOTIVATION Single-nucleus resolution multiome (snMultiome) assays concurrently profile gene expression and chromatin accessibility in the same nucleus. Yet regulatory inference from such analyses are difficult to scale, audit, and reproduce; moreover, as a field, snMultiomics and its toolset remains far from standardized. To address these challenges we developed FORGE, a configureable Nextflow…",
  "key_points": [],
  "editors_take": null,
  "illustration": null,
  "coverage": {
    "outlets": 2,
    "also_reported_by": [
      {
        "outlet": "bioRxiv",
        "title": "nanorepertoire: an end-to-end Nextflow pipeline for nanobody repertoire analysis",
        "url": "https://urgent.news/2026/09/16/nanorepertoire-an-end-to-end-nextflow-pipeline-for-nanobody",
        "published": "2026-09-16T00:00:00.000Z"
      }
    ]
  },
  "ai_generated": true,
  "disclaimer": "Summaries, key points and the editor’s take are written by software from other outlets’ reporting and may contain errors — always check the linked original."
}