OpenPretext

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Overview

O/E map

100%

Contigs

Scaffolds

Meta Tags

History

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3D Analysis

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Curation Progress

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Tracks

No tracks loaded. Press X to toggle visibility.

OpenPretext

Browser-based Hi-C contact map viewer and genome assembly curation tool

Have a .pretext file?

New to Hi-C curation?

Or explore an example

⌘K Command palette Workflow Guide Pattern Gallery

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Drop .pretext, .fasta, .bedgraph, or .json file

Script Console

Output will appear here...

AI Assist

Strategy:

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Name

Description

File checksums

A .pretext file carries no checksum of its own. OpenPretext checks the file's structure when it loads, which catches a file that is cut short or has a damaged tile. To confirm that every byte is intact, compare one of the values below with the checksum published alongside the file.

File
Size
MD5
SHA-256

Compare with a published checksum

Keyboard Shortcuts

Navigation

PanDrag

ZoomScroll

Jump to diagonalJ

Reset view (fit whole map)0 or Home

Modes

Navigate modeEsc

Edit modeE

Scaffold modeS

Waypoint modeW

Curation

Cut contig at cursorC

Join selected contigsJ

Invert selectedF

Reorder contigDrag

Select all⌘A

Undo⌘Z

Redo⌘⇧Z

Toggle exclusionH

Toggle comparisonP

Undo historyU

Auto sort⌥S

Auto cut⌥C

Waypoints

Next waypoint] or .

Previous waypoint[ or ,

Clear all waypointsDelete

Panels & Overlays

Command palette⌘K

Toggle mapM

Toggle gridL

Toggle tracksX

Next weak joinB

Previous weak join⇧B

Toggle info sidebarI

Script console`

File

Open file⌘O

Screenshot⌘S

Press ? or Esc to close

Recommended Workflow

Load

Open a .pretext file or load an example dataset

Explore

Pan and zoom the contact map to understand the assembly structure

Sort

Run Auto Sort (Cmd/Ctrl+K, then "Auto sort") to group contigs into chromosomes

Cut

Run Auto Cut (Cmd/Ctrl+K, then "Auto cut") to split misassembled contigs at breakpoints

Scaffold

Assign contigs to chromosomes using scaffold painting mode (S)

Analyze

Open the sidebar (I) and use its 3D Analysis section to compute insulation, compartments, and P(s) decay

Export

Export curated assembly as AGP, BED, or FASTA

Press Esc or tap outside to close

Preparing file

Assessment Results

Tutorials

Press Esc to close

Contigs

Scaffolds

Meta Tags

History

3D Analysis

Curation Progress

Tracks

OpenPretext

Keyboard Shortcuts

Navigation

Modes

Curation

Waypoints

Panels & Overlays

File

Tutorials

Hi-C Pattern Gallery