Nexus-G Documentation

Nexus-G is a local-first agentic bioinformatics workspace. The desktop client (GIAT engine) stores boards, downloads, BLAST databases, and run artifacts under ~/stDatApp. Heavy steps can stay on-laptop or burst to NG-Cloud Batch via BYOS storage and the NG-Cloud database stream.

The Workflow Builder lets you create repeatable multi-step pipelines — download → convert → BLAST → report — without writing code. Find it under Workflow Builder / Analysis Dashboard.

Tabs: Workflows list · Editor · Step Library · Jobs. Export/import workflows for handoff between machines.

Standard pipelines live under giat_package/pipelines. The path below is the standard pipeline — conversion, trimming + filtering, denoising, cluster, then ML-Predictor BLAST. Users can still create unlimited custom pipelines and insert their own tools and code with the Pipeline Agent wizard (discovery, install, format adaptation, save).

{
  "pipeline": "standard_sequence_blast",
  "version": "1.1.0",
  "stages": [
    { "id": "conversion", "tool": "format_converter" },
    { "id": "trim_filter", "tool": "read_trim_filter" },
    { "id": "denoise", "tool": "denoiser" },
    { "id": "cluster", "tool": "sequence_cluster" },
    { "id": "ml_predictor_blast", "tool": "ml_predictor_blast", "orchestration": "classic|agentic" }
  ],
  "outputs": [
    "03_blast/combined_enhanced.csv",
    "03_blast/combined_arbitration.csv",
    "blast_insights_report.html"
  ]
}

Agentic BLAST is a parallel orchestration path alongside Classic blast_package. It improves large-workload throughput (~90% faster than NCBI BLAST for supported cases) through GenBank enrichment/validation, accession caching, and ML-guided volume clustering — without exposing proprietary cloud internals.

Local Agentic runs require an Existing/External multi-volume BLAST DB. Classic remains switchable if Agentic cannot resolve binaries or databases.

The igtools package powers Analysis Explorer discovery, Entrez arbitration, Resolve-G enrichment, DeepLigate read prep, and related self-serve bench utilities exposed through Data Tools in the desktop app.

Cloud in Nexus-G means three things: your data credentials & NG-Cloud work bucket (BYOS), the deployment catalog for org Batch resources, and compute that can shift heavy BLAST to NG-Cloud Batch when enabled.

Opening soon.