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mjsull edited this page Sep 15, 2015 · 1 revision

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Create CAG file – Construct a CAG file (for more details see “Constructing a CAG” below)

Create Comparison – Create comparison (for more details see “Creating comparisons” below)

Load Assembly – Load FASTA/FASTG/CAG/LastGraph/.dot. For user generated .dot files or .dot generated using Abyss please concatenate with a FASTA file containing the forward sequence of each contig or scaffold this can be done from the command line using a command such as cat assembly.dot assembly.fa > assembly.contiguity.dot

Save Image – Save canvas as a postscript image

Change Working Directory – Change the working directory from .contiguity_wd

Cancel Running Process – Cancel any currently running processes

Exit – Cancel any currently running processes and quit Contiguity

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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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