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Creating Comparisons

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mjsull edited this page Sep 15, 2015 · 1 revision

Comparison can be created between a loaded assembly and a reference by selecting “Create comparison” from the “File” menu. If you have NCBI-BLAST+ installed and in your path comparisons can be generated on the fly by providing Contiguity with a reference file. Alternatively, an alignment file in BLAST’s tab-delimited (no header) format may be provided. Alignment results will be displayed if they satisfy the following default parameters:

Reference file – Reference file in FASTA or multiFASTA format

Comparison file – Alignment file in BLAST’s tab-delimited format

Minimum length – Only alignments of length (in base pairs) equal to or greater than this value will be shown

Minimum length (ratio) – Fraction of the contig sequence aligned to show alignment i.e. 0.5 means that an alignment needs to cover at least half the query to be shown

Minimum identity – Only alignments with an identity equal to or greater than this value (in percent) will be shown

Minimum bitscore – Only alignments with a bitscore equal to or greater than this value will be shown

Maximum evalue – Only alignments with an expect score lower than or equal to this value will be shown

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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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