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)
  • Have a pre and post test to evaluate program

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. Or using have a % of the reads to use
   • Combine multiple reads from organisms and see if can pull out individual genomes
   • 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

Timeline Plan

1. Finish maximum likelihood fitting of gaussian distribution (1.5 days max... if not done then, move on and come back to this later)
2. Choose assembly program. Considerations:
   • OLC or de Bruijn?
   • Can it run on the GCAT webserver?
   • What is the pipeline from contig to scaffold?
   • What kind of genome to use to develop parameters
3. Make forms and version of assembly program online... link of all of the forms and options
4. Work on tutorial text... begin with outline and fill in (I will also be taking notes for this section throughout the summer).
   • Throughout this process take notes of figure ideas or animations
   • STORYBOARD
5. Bring the web assembly pipeline and tutorial tool together in website... Considerations:
   • Easy to add to - like adding more modules (different assembly methods, genome comparisons, figures...)
   • Organized and easy to follow
6. Investigate genome comparison tools
   • Either locate one to implement on web or create one
7. Add this to existing 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.