Concepts
These pages are the educational frame for ChromoSort. They teach the ideas a new student or researcher should understand before choosing a command: what the evidence means, why the action is reasonable, and where the action can go wrong.
| Concept | Use it when |
|---|---|
| How to interpret dot plots | You need the visual grammar for reference/query alignment plots before deciding what action is justified. |
| How to decide when to fix a contig | You need to decide whether a suspicious alignment pattern is strong enough to justify splitting or cutting sequence. |
| How scaffolding works | You need to understand how ordered contigs become chromosome-scale scaffold records and why Ns are placeholders, not discovered sequence. |
| How gap filling works | You need to understand when graph or read evidence can replace scaffold Ns with sequence, and why ambiguous fills should stay unresolved. |
After the concept is clear, move to the Guides for ChromoSort-specific inputs, commands, reports, and reviewed application steps.