Multi-scaffold assembly joining

Reference-guided ordering of the scaffolds of a single fragmented assembly path into one joined sequence: map each scaffold to a reference mitogenome with minimap2, order + orient by reference coordinate, insert N-gap spacers where scaffolds are disjoint, and stitch per-position coverage to match.

Details

Pure-logic functions here back both the automatic Nextflow join (WF1) and the in-app manual override editor, so they take/return plain vectors and data.frames and never touch Shiny or the database directly.