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lecture_notes:04-07-2010 [2010/04/09 14:21]
karplus added correction for mistake I made in class about meaning of quality
lecture_notes:04-07-2010 [2010/04/11 22:47]
learithe
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   * Discusses Overlap and de-Bruijn graphs.   * Discusses Overlap and de-Bruijn graphs.
  
-454 Newbler assembler is entirely proprietary and almost nothing is known on how it works internally.+454 Newbler assembler is entirely proprietary and almost nothing is known on how it works internally ​(The only description is in the supplementary material of the original 454 method paper ((Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005.|http://​dx.doi.org/​10.1038/​nature03959)).
  
 Christy Hightower wants more feedback on the tools, to say good/​bad. ​ Feedback should be added to the wiki [[lecture_notes:​04-02-2010|lecture notes for her lecture]]. Christy Hightower wants more feedback on the tools, to say good/​bad. ​ Feedback should be added to the wiki [[lecture_notes:​04-02-2010|lecture notes for her lecture]].
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 === Quality === === Quality ===
  
- ​* ​Base-space and color-space ​comes with quality scores. +Base-space, flow-space, ​and color-space ​all come with quality scores. 
- * Flowspace does not have such? have to check. + 
- * SFS format is the flowspace format for input into the Newbler assembler. ​Does it have any independent ​quality ​measurement?+SFF format is the flowspace format for input into the Newbler assembler. ​It has quality ​scores for each base using standard -10 log<​sub>​10</​sub>​ probability. 
 +([[http://​www.ncbi.nlm.nih.gov/​Traces/​trace.cgi?cmd=show&​f=formats&​m=doc&​s=format#​sff|SFF format]])
  
 A large number of the assemblers throw away the quality data or only use it later. ​ Some use it to just throw away reads with low quality. A large number of the assemblers throw away the quality data or only use it later. ​ Some use it to just throw away reads with low quality.
lecture_notes/04-07-2010.txt · Last modified: 2015/09/14 18:40 by 68.180.230.228