Project Priority List
- 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
- 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
- Tutorial - include walkthrough and explain scaffolding as well
- Words/actual text
- Graphics - maybe make interactive graphics with html 5 technology... adobe flex, processing.js
- Genome comparison
- dotplot to visually compare contigs - program automatically rearranges all contigs of one to get as close to diagonal line as possible
- Effect of OLC vs de Bruijn - too technical?
- Scaffolding addition to website
- Finish maximum likelihood fitting of gaussian distribution (1.5 days max... if not done then, move on and come back to this later)
- 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
- Make forms and version of assembly program online... link of all of the forms and options
- 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
- 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
- Investigate genome comparison tools
- Either locate one to implement on web or create one
- 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.