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lecture_notes:04-29-2015 [2015/04/29 12:19]
chkan created
lecture_notes:04-29-2015 [2015/04/30 23:45] (current)
jennie
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-<​code>​ +======Team 5 Report: ​Discovar denovo======
-Discovar denovo ​is by the  Broad institute. It is a total pipeline, meaning that one needs to follow the sequencing as well as assembly protocols to obtain the best results. Most of the information is the in the PPT here. The notes below are supplemental.+
  
-Basic Outline: +=====Overview===== 
-Builds stacks +Discovar denovo is by the  Broad institute. It is a total pipeline, meaning that one needs to follow ​ 
-Filters out crap +the sequencing as well as assembly protocols to obtain the best results.  
-Builds consensus +Most of the information is the in the PPT here. The notes below are supplemental.
-Trys to merge stacks +
-Using pairwise windowsIf it finds a match it checks adjacent windows for overlap before they link them +
-Correct paired ends against each other +
-Then build using HQ pairs+
  
-Before Assembly+Basic Outline
-Spri beads size selection. +  * Builds stacks 
-No amplification in adapter phase. +  * Filters out crap 
-Wants a single library on an illumia machine.+  * Builds consensus 
 +  * Trys to merge stacks 
 +  * Using pairwise windowsIf it finds a match it checks adjacent windows for overlap before they link them 
 +  * Correct paired ends against each other 
 +  * Then build using HQ pairs
  
-Different Error Correction/​Gap filling steps: +=====Before assembly===== 
-Use sequential error correction increasing in difficulty to reduce computation +  * Spri beads size selection
-Look for isolated loser calls which means no LQ scores adjacent and corrects the scores up+  * No amplification ​in adapter phase. 
-Reduce quality scores ​in a sliding window.  ​Correct artifically high quality scores with adjacent low scores+  * Wants a single library on an illumia machine.
  
-Assembly: +=====Different error correction/​gap filling steps===== 
-Use the good founder pairs from previous steps to "​seed"​ building ​the genome.+  ​* ​Use sequential error correction increasing in difficulty ​to reduce computation 
 +  * Look for isolated loser calls which means no LQ scores adjacent and corrects ​the scores up. 
 +  * Reduce quality scores in a sliding window ​Correct artifically high quality scores with adjacent low scores
  
-</​code>​+=====Assembly===== 
 +  * Use the good founder pairs from previous steps to "​seed"​ building the genome.
lecture_notes/04-29-2015.1430335155.txt.gz · Last modified: 2015/04/29 12:19 by chkan