Guides

The Concepts explain why a pattern might justify action. These guides explain how to carry that reasoning into ChromoSort inputs, commands, reports, reviewed tables, and reproducible outputs.

If a command output looks wrong, start with Troubleshooting. If you need the visual grammar first, start with How to interpret dot plots.

Evidence And Interpretation

Guide	Use it when
Alignment evidence and the exact FASTA rule	You need to know when coords/PAF can be reused and when edited FASTA outputs require fresh alignments.
Choosing PAF or MUMmer coords	You need to choose, compare, or sanity-check whole-genome alignment evidence for a ChromoSort stage.
FASTA and evidence name matching	Plots, graph overlays, or command reports look empty because FASTA, PAF, coords, GFA, GAF, or Hi-C names may not match.
Reading ChromoSort audit tables	You need to translate TSV status labels into review decisions.
Inversions and orientation changes	You need to connect orientation patterns to ChromoSort review choices.
Assembly graph evidence	You need to read GFA segments, links, paths, walks, graph complexity labels, and graph guardrails.
hifiasm unitig-to-contig projection	You need to project unitig graph coordinates before they can annotate contig-axis plots.
Long-read PAF and GAF support	You need to interpret read bridges, breakpoint support, graph traversals, MAPQ filters, and advisory evidence.

Command Decisions And Review

Guide	Use it when
Sorting decisions and duplicate-overlap filtering	You need to understand kept, duplicate-overlap, terminal-overlap, split-candidate, and graph-guarded sort outcomes.
Sort, clean, fix, cut, or manual?	You need the least invasive ChromoSort action for the evidence in front of you.
Chimeric contig and breakpoint review	You need to review planner modes, smoothing, breakpoint penalties, selected contigs, and manual split boundaries.
Manual dashboard review	You need to move from browser review to a reproducible manual recipe.
Spreadsheet review tables	You need to accept, reject, or annotate evaluated fix, scaffold, or gapfill rows safely.
Scaffolding, gaps, and overlaps	You need to review inferred gaps, fixed gaps, negative gaps, overlaps, trim policies, or gap overrides.
Graph-supported gap filling	You need to decide whether graph paths are strong enough to replace scaffold N gaps.

Worked Review Guides

Guide	Use it when
Mostly-correct assembly cleanup	You want a conservative `chromo clean` path from raw FASTA through validation plots.
Suspected chimeric contig review	You want to go from a dot-plot signal to `eval fix`, manual review, reviewed splitting, re-alignment, and sorting.
Graph-aware scaffold and gapfill review	You want a combined GFA, GAF, Hi-C, reference-placement, scaffold, and gapfill review path.
Dataset handoff checklist	You need to package FASTA, alignments, graph evidence, review tables, plots, summaries, and notes for a new review session.