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Evidence views

Contact map

The contact map is read from .cool or .mcool and reprojected through the current AGP order, orientation, splits, moves, and copies. Available normalizations are:

  • None (Raw)
  • ICE (Balanced)
  • KR (Balanced)
  • VC (Coverage)
  • VC_SQRT

Normalization availability and cost depend on what is stored in the input and what must be computed. .mcool is preferred for large, multi-scale browsing because stored pyramid levels avoid repeatedly aggregating a single fine .cool level.

Color range can be entered manually or estimated with Auto. Changing color range affects rendering, not the underlying counts or AGP.

Coverage track

Coverage accepts four-column bedGraph-like records:

chrom  start  end  value

Blank lines, comments, and track/browser directives are ignored. Intervals must be valid 0-based half-open intervals. Values are length-weighted while records are projected through every matching AGP placement.

The track supports visibility, manual/automatic range controls, synchronized selection, pan, and zoom.

PAF synteny

PAF query names are matched to AGP source component IDs. The compact inspector preview can be expanded into an interactive split pane. The query axis follows the edited assembly and shared heatmap X viewport; the target axis remains the PAF reference coordinate system.

PAF is evidence only. Selecting a dotplot block selects the corresponding AGP unit, but the alignment does not automatically rename, orient, or move it.

GFA assembly graph

GFA segment names are matched to AGP component IDs. The graph panel provides three layouts:

  • Curation: chromosomes in AGP order, with unitigs kept in their assembly blocks;
  • Guided: the AGP backbone plus a local layer of GFA neighbors around the selection or heatmap focus;
  • Whole: topology-first graph layout, with AGP links as an optional layer.

Independent layers and filters include GFA links, endpoint 3D Contacts, AGP adjacency/gaps, homolog, non-homolog, anchor–unanchor, unplaced unitigs, and disconnected islands. Evidence layers start as display controls and do not rewrite AGP.

The Review queue is explicitly read-only. It can report endpoint conflicts, gap bridges, strong non-adjacent 3D-contact pairs, and copy ambiguities, together with what the evidence supports and its limits. Users may focus a candidate and then choose a separate assembly operation.

Unplaced GFA segments have an explicit placement dialog. Confirming placement is an AGP edit and is recorded in history; merely dragging graph nodes changes the graph layout, not the assembly.

Homolog regular expression

The global regular expression classifies scaffold names for GFA layouts. Capture group 1 defines a homolog column; capture group 2 orders chromosomes within the column. The default is:

(Chr\d+)g(\d+)

Use a pattern that matches the project's actual scaffold naming scheme. An invalid or non-matching pattern limits homolog-aware layout and filters; it does not change AGP identities.