Project Priority List

Genome Assembly

• Website modules that take in parameters and have a tutorial (probably want a few frames in webpage that can load individually)
  • At the end with the contig you compare them and also discuss the next steps of scaffolding (be sure to highlight the importance of having linker sequences)

1. Make the website to show changes in assembly based on changes in... - include pre analysis of raw reads with the scripts I have already made
   • kmer length
   • Lower coverage... using 1/2 reads
   • Not cleaning reads
2. Tutorial - include walkthrough and explain scaffolding as well
   1. Words/actual text
   2. Graphics - maybe make interactive graphics with html 5 technology... adobe flex, processing.js
   3. Animations
3. Genome comparison
   • dotplot to visually compare contigs - program automatically rearranges all contigs of one to get as close to diagonal line as possible
4. Effect of OLC vs de Bruijn - too technical?
5. Scaffolding addition to website

Phages DB (2nd priority)

• Take 2 groups of phages and pull out patterns
  • x % in group has 1 mobile element...
• Query based comparison
  • Give me gene X, and return list of gene and what % in one cluster... ect.