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lecture_notes:04-29-2015 [2015/04/29 12:19]
chkan
lecture_notes:04-29-2015 [2015/04/30 23:45] (current)
jennie
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-<​code>​+======Team 5 Report: Discovar denovo====== 
 + 
 +=====Overview=====
 Discovar denovo is by the  Broad institute. It is a total pipeline, meaning that one needs to follow ​ 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. ​ the sequencing as well as assembly protocols to obtain the best results. ​
Line 5: Line 7:
  
 Basic Outline: Basic Outline:
-Builds stacks +  * Builds stacks 
-Filters out crap +  ​* ​Filters out crap 
-Builds consensus +  ​* ​Builds consensus 
-Trys to merge stacks +  ​* ​Trys to merge stacks 
-Using pairwise windows. If it finds a match it checks adjacent windows for overlap before they link them +  ​* ​Using pairwise windows. If it finds a match it checks adjacent windows for overlap before they link them 
-Correct paired ends against each other +  ​* ​Correct paired ends against each other 
-Then build using HQ pairs +  ​* ​Then build using HQ pairs
- +
-Before Assembly: +
-Spri beads size selection. +
-No amplification in adapter phase. +
-Wants a single library on an illumia machine.+
  
-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/04-29-2015.1430335175.txt.gz · Last modified: 2015/04/29 12:19 by chkan