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Find paths

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mjsull edited this page Sep 15, 2015 · 1 revision

Find paths allows the user to find the shortest or all paths between all selected contigs. Simply select the contigs you would like to find paths between and then select “Find paths” from the “tools” menu. “Find paths” will search through the contig adjacency graph until it finds another selected contig or reaches the user defined node or base pair limit.

Illumina assembly mapped to a reference genome. There is a gap in the assembly between contigs 45 and 217 (panel a) by selecting both contigs and using the “Find paths” tool Contiguity is able to reconstruct this region of the chromosome (panel b).

Max bp – Depth of search in base pairs

Max node – Depth of search in contigs

Max paths – If this value is reached Contiguity will lower the amount of nodes being searched

Only find shortest path – Only report the shortest path (in base pairs) found

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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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