OpenPretext

A browser-based Hi-C contact map viewer and genome assembly curation tool. It reads native .pretext files, renders them with WebGL2, and lets you curate an assembly into chromosomes, with nothing to install.

Try it now  ·  Field guide to genome curation  ·  Report an issue

Open the app and click Load Example to explore a real koala assembly, or Start Tutorial for a guided walkthrough.

Contact map with contig sidebar, misassembly badges, annotation tracks, and analysis overlays.

What it is

OpenPretext is a browser-based alternative to PretextView, the Wellcome Sanger Institute desktop tool that genome assembly teams (Darwin Tree of Life, Vertebrate Genomes Project, Earth BioGenome Project) use to inspect Hi-C contact maps and arrange contigs into chromosomes. OpenPretext runs anywhere a browser does, needs no install, and adds scripting, automated curation, 3D genomics analysis, and an optional machine-learning enhancement server.

New to genome curation? Start with the field guide. It teaches you to read a contact map and recognize the common misassemblies before you touch the tool.

Quick start

Prerequisites: Node.js 22 or later.

git clone https://github.com/shandley/openpretext.git
cd openpretext
npm install
npm run dev

Open http://localhost:3000, then:

• Click Load Example to download and explore a real genome assembly.
• Click Open, or drag and drop a .pretext file from your computer.
• Click Start Tutorial for a guided walkthrough.

OpenPretext needs a local HTTP server; opening the files over file:// will not work (CORS and ES module loading). Use npm run dev while developing, or npm run build then npm run preview for a production build.

Learn

• Field guide to genome curation: a visual introduction to reading a Hi-C map, the misassembly signatures, and the curation workflow.
• In-app tutorials: 16 interactive lessons, from reading the map through guided curation to open-ended practice exercises. Open the app and click Start Tutorial.
• Pattern gallery: a reference of Hi-C patterns (clean diagonal, inversions, translocations, micro-chromosomes, and more) with descriptions and click-to-navigate.

Features

Rendering

WebGL2 contact map with tile-based level-of-detail, an LRU cache, and background decompression. Six color maps with keyboard cycling, adjustable gamma, a contig grid and edge labels, a click-to-navigate minimap, scaffold color bands, waypoint markers, annotation track overlays (line, heatmap, marker), and a comparison overlay of original versus curated boundaries. An observed/expected (O/E) view toggle divides out the distance-decay so long-range structure stands out (overview only; detail tiles stay raw at high zoom). A before/after view places the map as loaded beside the current curated arrangement.

Curation

Cut, join, invert, and move contigs with full undo and redo. Drag-and-drop reordering, a click / shift-range / ctrl-toggle selection system, contig exclusion (hide from export without deleting), scaffold painting for chromosome assignment, waypoint markers, batch operations (select by name or size, batch cut / join / invert, sort by length), and meta tags to classify contigs as haplotig, contaminant, unlocalised, or sex chromosome. Tags and exclusions follow a contig when it is cut; a join of an excluded contig with an included one is refused, because either result would change what is exported.

Automated curation

• Auto Sort (Union Find) scores every contig pair across four orientations using Hi-C link analysis, chains contigs into chromosome groups, and applies the needed inversions and reordering. Run it from the command palette, or Option+S (Alt+S) in edit mode.
• Auto Cut (breakpoint detection) finds misassembly breakpoints where the diagonal Hi-C signal drops and splits contigs there. Run it from the command palette, or Option+C (Alt+C) in edit mode.

A common recipe: run Auto Cut first to break misassemblies, then Auto Sort to group and orient the fragments. Every operation is individually undoable.

AI-assisted curation

Vision-based analysis through the Anthropic Messages API. It captures the current map, builds assembly context from contig ordering, metrics, and scaffold assignments, and returns runnable DSL command suggestions with one-click Run buttons. Ships with eight prompt strategies (general, inversion detection, scaffold assignment, fragmented assemblies, micro-chromosomes, analysis-guided, haplotig detection, telomere-aware), a custom-strategy editor, JSON export and import, and one-click browsing of community strategies from the panel. Your API key is stored locally and sent only to Anthropic.

3D genomics analysis

A suite of Hi-C metrics, all computed in a background Web Worker and exportable as BedGraph or TSV:

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