Contig Actions

seqhiker lets you adjust contig orientation and contig order from the right-click menu on a contig map strip.

This works in both:

  • browser mode, for the loaded genome

  • comparison view, for each genome row independently

Opening the menu

  • In browser mode, right-click a contig in the map track.

  • In comparison view, right-click a contig in that genome row’s contig map strip.

Available actions

The contig menu currently includes:

  • Reverse complement contig

  • Restore contig forward

  • Reverse complement all contigs

  • Restore all contigs forward

  • Move contig 1 to left

  • Move contig 1 to right

  • Move contig to start of genome

  • Move contig to end of genome

Some actions are disabled when they would have no effect, for example moving the leftmost contig further left.

Browser mode behavior

In browser mode, contig actions update the loaded genome layout immediately.

That includes:

  • the concatenated genome layout in concat mode

  • the contig list used by Go

  • the map strip and viewport overlay

  • annotations

  • read/depth/gc/variant tracks

Reverse-complementing a contig also flips feature orientation and updates the displayed reference sequence for that contig.

Comparison view behavior

In comparison view, contig actions apply only to the selected genome row.

When a contig is reverse-complemented or moved, seqhiker rebuilds that row’s concatenated coordinates and refreshes:

  • annotations on that genome

  • pairwise matches connected to neighboring genomes

  • comparison detail lookups for affected blocks

Genome row order is separate from contig order:

  • drag the row handle to reorder whole genomes

  • use the contig right-click menu to reorder contigs within one genome

Notes

  • Browser mode and comparison mode keep separate state.