Graph-based cancer genome scaffolding tool

SKYPE generates following results.

• Circos plot, which shows copy number of chromosomes
• Virtual SKY diagram, which shows most reasonable combinations of mutated chromosome
  
  

SKYPE implements following steps to achieve above results.

• Classify contigs as their mutational role and prune unnecessary parts
• Compress contigs by their most significant terminal node (NClose)
• Build breakend graph by connecting NClose nodes and telomere nodes
• Find all simple telomere-to-telomere paths of breakend graph
• Recover full path with normal contigs
• Optimize copy number of each paths by using customized SI-NNLS algorithm
• Visualize results

Prequisites

It is recommended to use ACCtools pipeline, rather than using SKYPE alone.

Results are saved as 2 png files.

• <SKYPE result folder>/<CELL_LINE_RESULT_FOLDER>/total_cov.png : Circos plot
• <SKYPE result folder>/<CELL_LINE_RESULT_FOLDER>/virtual_sky.png : Virtual SKY diagram

Arguments and Variables

First argument defines cell line to analyze. Second argument(optional) defines the folder to save SKYPE result. Change THREAD variable

Example

Please check README.md in ACCtools pipeline