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Creating Scaffolds from a PacBio assembly

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mjsull edited this page Sep 15, 2015 · 1 revision

Once the assembly has been loaded and displayed on the canvas select “Self-comparison” from the “View” menu, ensure that you check the “Only show edge hits” checkbox. Order and orientate the contigs in the correct direction and then select contigs you wish to make up the scaffold. Contiguity will remove merge the contigs removing the overlapping sequence. Contiguity uses the sequence from the larger contig if there are mismatches in the overlap.

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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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