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Constructing a Contig Adjacency Graph

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mjsull edited this page Sep 15, 2015 · 1 revision

A Contig Adjacency Graph (CAG) is a directed graph where each contig in a de novo assembly is represented as two nodes (forward and reverse strand). A directed edge is created from node A to node B if the sequence represented by node B occurs directly after the sequence represented by node A.

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  1. Introduction to Contiguity
  2. Requirements
  3. Installation
  4. Citing Contiguity
  5. Workflow and Examples
  6. Finishing a PacBio HGAP assembly
  7. Ordering contigs
  8. Finding passenger genes
  9. Identifying plasmid contigs
  10. Menu overview
  11. File
  12. View
  13. Tools
  14. Viewing the Assembly
  15. Canvas overview
  16. Context menus
  17. Creating comparisons
  18. Comparison to a reference
  19. Self comparison
  20. Finding paths
  21. Creating scaffolds
  22. Creating scaffolds from a CAG
  23. Creating scaffolds from a PacBio Assembly
  24. Constructing a Contig adjacency graph
  25. CAG creation GUI
  26. CAG creation command-line

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