Project Priority List
From GcatWiki
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)
- 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
- Tutorial - include walkthrough and explain scaffolding as well
- Words/actual text
- Graphics - maybe make interactive graphics with html 5 technology... adobe flex, processing.js
- Animations
- 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
Timeline
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.