Difference between revisions of "Project Priority List"
From GcatWiki
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(→Genome Assembly) |
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**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) | **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... kmer length | + | #Make the website to show changes in assembly based on changes in... |
| − | # | + | #*kmer length |
| − | # | + | #*Lower coverage... using 1/2 reads |
| + | #*Not cleaning reads | ||
#Tutorial | #Tutorial | ||
#Genome comparison | #Genome comparison | ||
Revision as of 16:20, 13 June 2011
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...
- kmer length
- Lower coverage... using 1/2 reads
- Not cleaning reads
- Tutorial
- 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
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.
