OpenPretext
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OpenPretext

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

New to Hi-C curation?
Have a .pretext file?
Explore examples Browse the specimen grid below
Example Datasets
⌘K Command palette   E Edit mode   L Toggle grid   Workflow Guide
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Drop .pretext, .fasta, .bedgraph, or .json file
Script Console
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Keyboard Shortcuts

Navigation

PanDrag
ZoomScroll
Jump to diagonalJ
Reset viewHome

Modes

Navigate modeN
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
Toggle info sidebarI
Script console`

File

Open file⌘O
Screenshot⌘S
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Recommended Workflow

1
Load
Open a .pretext file or load an example dataset
2
Explore
Pan and zoom the contact map to understand the assembly structure
3
Sort
Run Auto Sort (Cmd+K → "Auto sort") to group contigs into chromosomes
4
Cut
Run Auto Cut to split misassembled contigs at breakpoints
5
Scaffold
Assign contigs to chromosomes using scaffold painting mode (S)
6
Analyze
Compute insulation, compartments, and P(s) decay to validate
7
Export
Export curated assembly as AGP, BED, or FASTA
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Tutorials

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